From: yjcoshc (yjcoshc_at_gmail.com)
Date: Wed Dec 05 2018 - 19:45:11 CST
If you really need Cartesian coordinates of ALL atoms in the simulation,
you can create a copy of your pdb input file to refatoms.pdb and mark
the occupancy column with 2.0 for all atoms and use
in your colvars input file. For the calculation based on these
coordinates, you can use either the scriptedFunction or customFunction
Then again, requesting coordinates of all atoms may greatly slow down
the simulation, so actually we only mark the atoms we need in the atomsFile.
在 2018/12/6 上午8:39, Faramarz Joodaki 写道:
> Dear Haochuan,
> Thank you again for your guidance and sorry for my late response!
> Yes, NAMD can save dv evey step. I think for this parameter, I am
> going to save them and then apply my calculation on them.
> I have a question about colvars module. If covalrs module have an
> access to all coordinated of atoms, how can I apply my calculation on
> Best Regards,
> On Tue, Nov 27, 2018 at 8:44 PM yjcoshc <yjcoshc_at_gmail.com
> <mailto:yjcoshc_at_gmail.com>> wrote:
> Hello Faramarz,
> As far as I know, the aMD's dV is not collected to the colvars
> module. Maybe you want to use your own histogram code and the dV
> to reweight the trajectory on the fly. Actually I have tried to
> modify the NAMD's code to make it working with the histogram in
> 1. Export dV from NAMD's TCL interface and implement a
> getaMDWeight TCL command to get the dV in the NAMD configuration
> file every step;
> 2. Modify the histogram bias in colvars to make it accept the
> weight on the fly (the weight can be set by calling cv bias histo1
> reweight w);
> 3. Modify the NAMD configuration accordingly.
> In this way I have to set stepspercycle to 1 and use a TCL loop
> with "run 1" to reweight the histogram on the fly, so it's rather
> A faster way may be to collect the dV to colvars module through
> the C++ interface (NAMD's GlobalMaster) directly. The NAMD's code,
> however, are rather undocumented and currently I don't work on it.
> If you have some better ideas please let me know.
> Haochuan Chen
> 在 2018/11/28 上午6:10, Faramarz Joodaki 写道:
>> Dear Haochuan and Jerome,
>> Thank you for your response and guidance!
>> My calculation will not be expensive and I need all all atom
>> coordinates and some calculate properties by NAMD such as dv in
>> the accelerated MD. I will check colvars module.
>> Best Regards,
>> On Mon, Nov 26, 2018 at 7:27 AM Jérôme Hénin
>> <jerome.henin_at_ibpc.fr <mailto:jerome.henin_at_ibpc.fr>> wrote:
>> To add to Haochuan's remark: the best way to do it will
>> vastly depend on what you are calculating, and what it
>> depends on: positions? velocities? forces? few atoms, many
>> atoms, all atoms? box size? pressure? Is it an expensive
>> calculation? Do you need to parallelize it?
>> On Sun, 25 Nov 2018 at 02:25, yjcoshc <yjcoshc_at_gmail.com
>> <mailto:yjcoshc_at_gmail.com>> wrote:
>> Hi Faramarz,
>> If you only require the atomic coordinates and the
>> current step, you can
>> utilize the colvars module. The usage can be found in the
>> NAMD manual.
>> Haochuan Chen
>> 在 2018/11/24 上午2:58, Faramarz Joodaki 写道:
>> > Hi everyone!
>> > I would like to do some calculations on trajectory for
>> each step of a
>> > MD simulation. It is a long MD simulation so saving all
>> steps in dcd
>> > file is impossible.
>> > Hence, I need to add some codes to the source code of
>> NAMD to
>> > calculate some properties during MD simulations
>> (Runtime). I was
>> > wondering if there is a proper way to do that.
>> Actually, I can go
>> > inside the source code and change or add my C code but
>> I am looking
>> > for an efficient way to do that such as linking my code
>> to the source
>> > code of NAMD. I would be so grateful if you could guide
>> me with this
>> > matter.
>> > Best Regards,
>> > Faramarz
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