From: James Starlight (jmsstarlight_at_gmail.com)
Date: Thu Sep 05 2013 - 10:52:29 CDT
One extra question about solvation
I've forced with the problem of the expanding of my system in Z dimension (
adding some addition solvent)
In fact I've used membrane made by VMD and add some water by means of
solvate plugin. Than I equilibration that hydrated bilayer and inserted
protein into it. After visualization I've decided to add some more water to
increase Z dimension of my system. Unfortunately second solvation of that
membrane by means of solvate plugin ended with the error because of the
overlapping segment names (WT1- WT10 produced during first solvation). How
I could remove all old water (WT1-WT10) from both pdb and psf files and
make new PSF for the de-solvated system ?
James
2013/9/5 James Starlight <jmsstarlight_at_gmail.com>
> I've noticed the possible source of such error could arise from unproper
> minimization cycle.
>
> I've noticed that coordinates of the lipid and water didn't change during
> minimization cycle (although I didn't use any fix or restraints options in
> the conf file) such problem occurred only in case of the protein+solvent
> complex (in case of the minimization of the pure solvent the coordinates of
> the lipid tales as well as water change rapidly during minimization ).
>
> By the way does someone know possible source of the pre-equilibrated
> bi-layers made in charm params?
>
> Thanks for help
>
> James
>
>
> 2013/9/5 James Starlight <jmsstarlight_at_gmail.com>
>
>> Aron, thanks for suggestions!
>>
>> I've done all such operations but the results the same.
>>
>> If it possible I can share pdb as well as psf files of my complex
>> produced after ionization by VMD.
>>
>> Perhaps some problems might be also due to the insertion (automate
>> generation of the complex psf which have been done according to the script
>> provided in the
>> http://users.mccammon.ucsd.edu/~rlaw/ctbp_workshop_rlaw.htm ) If someone
>> have modified version of such script for quick insertion and deletion of
>> the lipids in the aligned bi-layer I'll be thankful for it as well as for
>> example conf file for production run of the protein-lipid system made with
>> ch27 params
>>
>> Thanks again,
>>
>> James
>>
>>
>> 2013/9/4 Aron Broom <broomsday_at_gmail.com>
>>
>>> just on the PBC thing, although I somewhat doubt it's the answer. Your
>>> cellBasisVector values don't agree with what you posted from VMD. For
>>> instance, you have cellBasisVector3 as 98.2, but that value from VMD should
>>> be (93.664 - 0.594) which is 93.07, the others are off by much less.
>>>
>>> Some other things to try before the restraints:
>>>
>>> - increase minimization steps (go 10x what it currently is maybe)
>>> - decrease timestep (go to 0.5 for instance)
>>> - decrease temperature (start at something quite low like < 100K)
>>>
>>> Also, you said analysis doesn't reveal artifacts, but if there is a
>>> constraint failure, then something went flying off at high speed. So you
>>> might want to decrease you DCDFrequency or whatever the variable is called
>>> so you can see what is leading to the problem, particularly if this is
>>> happening early on.
>>>
>>> ~Aron
>>>
>>>
>>> On Wed, Sep 4, 2013 at 12:16 PM, James Starlight <jmsstarlight_at_gmail.com
>>> > wrote:
>>>
>>>> Dear NAMD Users!
>>>>
>>>>
>>>> Recently I've forced with the problem of simulation membrane protein
>>>> system.
>>>>
>>>> I've done all steps according to the official tutorial
>>>>
>>>> 1) building POPE membrane using VMD
>>>>
>>>> 2) generated PSF files of my protein
>>>>
>>>> 2) inserted protein into membrane and removed overlapped lipids
>>>>
>>>> 3)solvated and ionized my system using VMD
>>>>
>>>> Than I've minimized my system and tried pack lipids but simulation have
>>>> been crashed
>>>>
>>>> on this step I've froze all water ion and protein atoms and run short
>>>> simulation in NPT according to the tutorial parameters.
>>>>
>>>> as the result I've obtained
>>>>
>>>> Info: ABSOLUTE IMPRECISION IN FAST TABLE ENERGY: 1.69407e-21 AT 11.9974
>>>> Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 1.13046e-16 AT 11.9974
>>>> Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.000290274 AT
>>>> 0.251946
>>>> Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946
>>>> Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT
>>>> 0.251946
>>>> Pe 2 hosts 15 local and 15 remote patches for pe 2
>>>> Pe 3 hosts 15 local and 15 remote patches for pe 2
>>>> Pe 1 hosts 10 local and 10 remote patches for pe 2
>>>> Pe 0 hosts 23 local and 22 remote patches for pe 2
>>>> Info: useSync: 1 useProxySync: 0
>>>> Info: Startup phase 10 took 0.037595 s, 102.809 MB of memory in use
>>>> Info: Startup phase 11 took 0.000133991 s, 102.973 MB of memory in use
>>>> Info: Startup phase 12 took 0.000496864 s, 103.18 MB of memory in use
>>>> Info: Finished startup at 1.20948 s, 103.34 MB of memory in use
>>>>
>>>> TCL: Running for 250000 steps
>>>> Pe 2 has 63 local and 62 remote patches and 1701 local and 1674 remote
>>>> computes.
>>>> ERROR: Constraint failure in RATTLE algorithm for atom 35875!
>>>> ERROR: Constraint failure; simulation has become unstable.
>>>> ERROR: Exiting prematurely; see error messages above.
>>>> ====================================================
>>>>
>>>> its remarkable that such error have occurred even with applied position
>>>> restraints to ALL atoms of my system. In addition I've tried to make such
>>>> packing for pure hydrated lipids but forced with the same error too.
>>>>
>>>>
>>>> Might it be due to some problems with the PBC definition (I've done
>>>> manually definition of the xyz dimensions using vmd as you can see below
>>>>
>>>> atomselect0
>>>> >Main< (GPRC_namd) 2 % measure minmax $everyone
>>>> {1.0085545778274536 0.6706096529960632 0.593999981880188}
>>>> {104.46700286865234 102.0479965209961 93.66400146484375}
>>>>
>>>> measure center $everyone
>>>> 52.83515548706055 51.502288818359375 46.488792419433594
>>>>
>>>> and than defined that in the conf file:
>>>>
>>>>
>>>> cellBasisVector1 103.1 0 0
>>>> cellBasisVector2 0 100.9 0
>>>> cellBasisVector3 0 0 98.2
>>>> cellOrigin 52.80777359008789 51.45378112792969 46.48970031738281
>>>>
>>>>
>>>> during analysis of the minimization I've not observed any artifacts.
>>>>
>>>> What also membrane simulation options should I take into account?
>>>>
>>>>
>>>> Thanks for help,
>>>>
>>>> James
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Aron Broom M.Sc
>>> PhD Student
>>> Department of Chemistry
>>> University of Waterloo
>>>
>>
>>
>
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