VMD-L Mailing List

From: Anthony Cruz-Balberdy (anthonycruzpr_at_gmail.com)
Date: Tue Jan 26 2021 - 11:25:45 CST

Hi Rakesh,

Is difficult to assess the situation without knowing more about your
simulation but I think that the problem could be the dimensions of the
simulation box and not the "pbc wrap" command. To confirm, after doing the
"pbc warp" try to draw the simulation box and check that your box is big
enough in the direction where you are seen the fluctuations. If your
simulation box is not big enough in that direction, then you will see the
fluctuations no matter what you do because the cluster is growing in that
direction.

I had a similar problem with a simulation of the self-assembly of a cyanine
dye.

Regards,
Anthony

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On Jan 26, 2021, at 1:51 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> I think there were other recent inquiries about PBC wrapping
> and/or rewrapping of LAMMPS trajectories on VMD-L, I'd suggest
> searching the list for these recent postings. I think it came
> up sometime just in the last half year or so if I'm not mistaken.
> I'm not a LAMMPS expert, so I can't provide any specific guidance.
>
> Best regards,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Thu, Jan 14, 2021 at 06:11:38PM +0530, Rakesh K wrote:
>
>> Hi all,
>>
>> I have simulated polymer system with attractive and repulsive LJ using PBC
>> conditions in LAMMPS. I wanted to wrap the simulation in the periodic box
>> in VMD. I used the following command.
>>
>> pbc wrap -center com -centersel "residue 1" -compound res -all
>>
>> Different residues and types were used in centersel and wrapped, but the
>> resulting trajectory will have fluctuating positions of polymers from one
>> side of the box to another side.
>> This looks bad if all the polymers are of one cluster and they split for
>> some time due to packing.
>>
>> Is there any set of commands or ways to wrap the system such that the
>> system wraps correctly?
>>
>> Thanks and Regards,
>> Rakesh K.
>> Research Scholar,
>> IIT Bombay.
>>
>