Re: Creating an infinite graphene sheet

From: jashnvareh 1395 (jashnvareh1395_at_gmail.com)
Date: Sat May 19 2018 - 20:23:17 CDT

Hi Josh, Thanks a lot. I did "useConstantArea yes" and regarding the
boundaries everything is OK and I have an infinite graphene sheet.
Just I see that during the simulation, the graphene sheet in the primary
cell drifts from initial place geting out of the primary cell and also
moving up/down as well. I didn't see such drifts during the simulation of
infinite membrane. I copy the configuration file with the hope to get
your suggestion on that:

# inputs
coordinates = solvate.pdb
structure = solvate.psf

parameters = par_all27_prot_lipid.prm
paraTypeXplor off
paraTypeCharmm on

set inputname gra-lser_min-heat
bincoordinates $inputname.coor
binvelocities $inputname.vel
extendedSystem $inputname.xsc

DCDfile = gra-lser_NPT.dcd
DCDfreq = 1000
outputname = gra-lser_NPT
restartname = gra-lser_NPT
restartfreq = 1000
outputEnergies = 1000
outputTiming = 1000

wrapWater on
wrapNearest off

#temperature 300 commented because we are restarting from the .vel
timestep = 1.0
stepspercycle = 20

cutoff = 12.0
switching on
switchdist = 10.0
pairlistdist = 14.0
splitPatch = hydrogen
hgroupCutoff = 2.5
pairlistsPercycle = 10
exclude = scaled1-4
COMmotion no
zeromomentum no
dielectric 1.0
1-4scaling 1.0

rigidBonds = all #SHAKE on
useSettle on # faster than SHAKE algorithm on water

fullElectFrequency = 1
nonbondedFreq = 1

MTSAlgorithm verletI
longSplitting c1

PME yes
PMEGridSpacing 1.0
#cellOrigin -0.003 0.000 -0.008 # to be commented next time when restarting
#cellBasisVector1 108.0 0 0
#cellBasisVector2 0 108.0 0
#cellBasisVector3 0 0 108.0

set temp 310
langevin on
langevinTemp $temp
langevinDamping 2
useGroupPressure yes
useConstantArea yes
useFlexibleCell yes
margin 5
#useConstantArea yes
LangevinPiston on
LangevinPistonTarget 1
LangevinPistonPeriod 200
LangevinPistonDecay 100
LangevinPistonTemp $temp

run 1000000

با احترام
دکتر زینب محمد حسینی
مدیریت آموزشی و پژوهشی مرکز آموزش عالی کاشمر

On Wed, May 16, 2018 at 6:00 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> Two things that might help: did you regenerate angles and dihedrals after
> adding the bonds? Topotools has a "guessangles" and "guessdihedrals" for
> this, which will work to keep deformations to a minimum. Also, when
> simulating in NPT, are you using a normal isotropic ensemble or a
> semi-isotropic one? You've built a sheet, which means a semi-isotropic
> barostat (useConstantRatio yes) is likely more appropriate. If you use an
> isotropic ensemble, you may end up crushing your sheet in an unnatural way.
>
> -Josh
>
>
>
> On 2018-05-15 23:54:08-06:00 jashnvareh 1395 wrote:
>
> Hi Josh,
> Yes it's exactly what you said. Thank you so much to making the things
> clear..
> In my case I did exactly the same as what you said. using "topo addbond"
> command I made the connections between primary cell and it's images. I did
> the preparation protocol (minimization and heating up the system). Within
> this procedure everything is OK and the connections are kept in the way
> that I have an infinite sheet. I then do the NPT simulation to make sure
> about the uniform density of the water molecules.
> This step destroyed the the bonds between primary cell and it's images. I
> even tried fixing the carbons and doing NPT but finally only the waters
> shrink and if I then do normal NVT for the data collections I ends up
> with a non-uniform water box again. Any suggestion on that?
>
> با احترام
> دکتر زینب محمد حسینی
> مدیریت آموزشی و پژوهشی مرکز آموزش عالی کاشمر
>
> On Sun, May 13, 2018 at 11:28 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov
> > wrote:
>>
>> Yeah, VMD doesn't have a clean way of visualizing bonds across periodic
>> images. Basically all VMD knows how to do is to link together atoms
>> *within* a periodic unit cell. Since atoms on the left and right edges
>> should be "bonded", the result is bonds that stretch across the periodic
>> unit cell. When simulated, the pbc is correctly taken into account, and
>> they'll act like short bonds. So basically this looks perfectly normal to
>> me. When visualizing cellulose, I'll often switch to VDW just so it doesn't
>> look dumb.
>>
>> -Josh
>>
>>
>>
>> On 2018-05-13 10:24:00-06:00 jashnvareh 1395 wrote:
>>
>> Sorry .. I made a mistake .. its pbwithin and here is the commands I used:
>> set sel [atomselect top "pbwithin 3 of index 47"]
>> atomselect4
>> $sel get index
>> 0 1 44 45 46 47 48 49 92 94 95 961 1007
>> All the indices obtained are in the primary cell and not in the periodic
>> image..
>> I attached a render image (img.tga). The orange is related to the above
>> indeces.. Then if I connect one to another I get a
>> long bond like in img2.tga
>>
>> با احترام
>> دکتر زینب محمد حسینی
>> مدیریت آموزشی و پژوهشی مرکز آموزش عالی کاشمر
>>
>> On Sun, May 13, 2018 at 8:23 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com
>> > wrote:
>>>
>>> Obviously for each atom you should exclude the atom itself from the
>>> selection. Also, you should set the periodic boundary conditions correctly
>>> for VMD. Why don't you experiment first with a linear polymer, and do the
>>> more time-consuming 2D graphene sheet later?
>>>
>>> On Sun, May 13, 2018 at 11:34 AM, jashnvareh 1395 <
>>> jashnvareh1395_at_gmail.com> wrote:
>>>>
>>>> Thanks a lot for the reply. Maybe I'm wrong but when I try for example
>>>> "pbwithin 3 of my edge selection" it gave me the indices within the same
>>>> sheet and not in it's periodic images. if I add bond for those atoms I
>>>> get a long bond from one edge to the opposite edge of the primary sheet..
>>>> May you guide me on that?
>>>>
>>>> با احترام
>>>> دکتر زینب محمد حسینی
>>>> مدیریت آموزشی و پژوهشی مرکز آموزش عالی کاشمر
>>>>
>>>> On Sun, May 13, 2018 at 7:38 PM, Giacomo Fiorin <
>>>> giacomo.fiorin_at_gmail.com> wrote:
>>>>>
>>>>> For the edge of the nearest periodic image, I suggested you to use an
>>>>> atom selection based on "pbwithin" for each of the edge atoms.
>>>>>
>>>>> Giacomo
>>>>>
>>>>> On Sun, May 13, 2018 at 3:11 AM, jashnvareh 1395 <
>>>>> jashnvareh1395_at_gmail.com> wrote:
>>>>>>
>>>>>> Thanks a lot for your prompt answers,
>>>>>> Hi Giacomo,
>>>>>> My question is that in the "topo addbond" command which atom id
>>>>>> should be selected for the periodic image?
>>>>>> I have the atom id of my real sheet at the edges but how about the
>>>>>> atom id for the periodic image?!
>>>>>> All the Best,
>>>>>> Zeynab
>>>>>>
>>>>>> با احترام
>>>>>> دکتر زینب محمد حسینی
>>>>>> مدیریت آموزشی و پژوهشی مرکز آموزش عالی کاشمر
>>>>>>
>>>>>> On Sun, May 13, 2018 at 1:57 AM, Vermaas, Joshua <
>>>>>> Joshua.Vermaas_at_nrel.gov> wrote:
>>>>>>>
>>>>>>> Yes. This how we do things like make infinite cellulose, although we
>>>>>>> have the benefit of specific patches to make the chemistry we are
>>>>>>> interested in. The most annoying part is making sure that you don't
>>>>>>> inadvertently introduce a defect at the boundary of the periodic cell. For
>>>>>>> graphene, this means making sure that your original sheet matches nicely at
>>>>>>> the edges.
>>>>>>>
>>>>>>> -Josh
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 2018-05-12 12:25:04-06:00 owner-namd-l_at_ks.uiuc.edu wrote:
>>>>>>>
>>>>>>> Hi, you could try using TopoTools to add bonds between atoms at the
>>>>>>> edges of the sheet. You could select them automatically, or using spatial
>>>>>>> criteria. To find the nearest neighbor of each edge atom, a selection
>>>>>>> based on "pbwithin" should help.
>>>>>>>
>>>>>>> Giacomo
>>>>>>>
>>>>>>> On Sat, May 12, 2018 at 11:34 AM, jashnvareh 1395 <
>>>>>>> jashnvareh1395_at_gmail.com> wrote:
>>>>>>>>
>>>>>>>> Dear all,
>>>>>>>> I want to run the simulation of an infinite graphene sheet solvated
>>>>>>>> in water.
>>>>>>>> I don't know how to create an infinite sheet with it's periodic
>>>>>>>> images.
>>>>>>>> Should I add bonds between graphene and it's periodic images or is
>>>>>>>> not needed?
>>>>>>>> I searched within the forum but couldn't find a clear answer.
>>>>>>>> Would be so much thankful to help me..
>>>>>>>> All the Best,
>>>>>>>> Zeynab
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Giacomo Fiorin
>>>>>>> Associate Professor of Research, Temple University, Philadelphia, PA
>>>>>>> Contractor, National Institutes of Health, Bethesda, MD
>>>>>>> http://goo.gl/Q3TBQU
>>>>>>> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgoo.gl%2FQ3TBQU&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C9aeb02ac3f194ab68a6608d5b835ac36%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636617463035631609&sdata=y%2BjikkoGuqDMiQkZxpeGi5OtCckmgjmT2PbYEoZbLpk%3D&reserved=0>
>>>>>>> https://github.com/giacomofiorin
>>>>>>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fgiacomofiorin&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C9aeb02ac3f194ab68a6608d5b835ac36%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636617463035641614&sdata=jNz87wupVjyfyQmhBaqfv7OuRrEXXj3vGAUDOa4ZEPs%3D&reserved=0>
>>>>>>>
>>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Giacomo Fiorin
>>>>> Associate Professor of Research, Temple University, Philadelphia, PA
>>>>> Contractor, National Institutes of Health, Bethesda, MD
>>>>> http://goo.gl/Q3TBQU
>>>>> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgoo.gl%2FQ3TBQU&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C035a80490c8b44d43c5308d5b8edecbe%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C1%7C636618254403833048&sdata=tycv5uHiWD1MNN9Zc6qyHzJcUygwBJqBdYYrarKf4o8%3D&reserved=0>
>>>>> https://github.com/giacomofiorin
>>>>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fgiacomofiorin&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C035a80490c8b44d43c5308d5b8edecbe%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C1%7C636618254403833048&sdata=ycWkeCzNhYUi3aHSAl2IHLd0rnGj702wkLPhgl%2Fc120%3D&reserved=0>
>>>>>
>>>>
>>>
>>>
>>> --
>>> Giacomo Fiorin
>>> Associate Professor of Research, Temple University, Philadelphia, PA
>>> Contractor, National Institutes of Health, Bethesda, MD
>>> http://goo.gl/Q3TBQU
>>> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgoo.gl%2FQ3TBQU&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C035a80490c8b44d43c5308d5b8edecbe%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C1%7C636618254403833048&sdata=tycv5uHiWD1MNN9Zc6qyHzJcUygwBJqBdYYrarKf4o8%3D&reserved=0>
>>> https://github.com/giacomofiorin
>>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fgiacomofiorin&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C035a80490c8b44d43c5308d5b8edecbe%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C1%7C636618254403833048&sdata=ycWkeCzNhYUi3aHSAl2IHLd0rnGj702wkLPhgl%2Fc120%3D&reserved=0>
>>>
>>

This archive was generated by hypermail 2.1.6 : Sat Sep 21 2019 - 23:19:37 CDT