Re: Strange Bond Behavior Question

From: Brian Radak (brian.radak_at_gmail.com)
Date: Fri Jun 22 2018 - 16:12:30 CDT

CHARMM and NAMD do indeed have very different PBC conventions (actually
AMBER too, probably GROMACS?).

The only procedure from CHARMM-GUI that I know works with NAMD is to use
the MD input generator and specifically request NAMD inputs. You then need
not only the XPLOR format PSF (CHARMM format should not work as expected in
NAMD!), but also the "pbcrotated" input files, both the PDB and XSC. Other
inputs will not wrap as expected in NAMD.

On Fri, Jun 22, 2018 at 5:08 PM, João Ribeiro <jribeiro_at_ks.uiuc.edu> wrote:

> Hi Kelly,
>
> that really sounds strange, especially because "They seem to be stretching
> and bonding to other lipid atoms"
> is
> vague and creation of bonds is impossible.
> ​ ​
> Now, if you generated the bilayer in CHARMM-GUI, I am pretty sure that the
> boundary conditions will be wrong. QwikMD doesn't have a way to detect the
> axis of membranes generated by other programs, so I will assume that you
> have water surrounding your system, even the hydrophobic region of the
> membrane.
>
> What happens if you run the simulation with the psf and pdb files
> generated by CHARMM-GUI? Do you observe the same? If you don't, I would
> suggest for you to use those psf and pdb files with the configuration files
> originated by CHARMM-GUI, or use QwikMD configuration files as templates,
> changing the necessary information about your system.
>
> Best
>
> Joao
>
>
> On Fri, Jun 22, 2018 at 3:46 PM McGuire, Kelly <mcg05004_at_byui.edu> wrote:
>
>> This is a question for both VMD and NAMD support, so I am sending it to
>> both. I used QwikMD to set up a simulation, and
>>
>> something I have never seen before has occurred. I placed a membrane
>> protein in a 100x100 DMPC bilayer using
>>
>> CHARMM-GUI, and then I used that PDB to set up a simulation in QwikMD.
>> Upon observation of the minimization, annealing, and
>>
>> equilibration DCD files, I noticed the lipid bonds doing something very
>> odd. They seem to be stretching and bonding to other
>>
>> lipid atoms. I tried attaching pictures, but I don't see it posted to
>> the mailing list. I didn't change anything in the minimize, anneal,
>>
>> and equilibrate scripts that QwikMD produces, and I've never seen this
>> before with those simulations with these generated scripts...
>>
>>
>>
>>
>>
>>
>>
>> *Kelly L. McGuire*
>>
>> *PhD Scholar*
>>
>> *Department of Physiology and Developmental Biology*
>>
>> *Brigham Young University*
>>
>> *LSB 3050*
>>
>> *Provo, UT 84602*
>>
>>
>>
>
> --
> ……………………………………………………...
> João Vieira Ribeiro
> Theoretical and Computational Biophysics Group
> Beckman Institute, University of Illinois
> http://www.ks.uiuc.edu/~jribeiro/
> jribeiro_at_ks.uiuc.edu
> +1 (217) 3005851
>

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