VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Dec 15 2009 - 10:45:27 CST

Hi Francesco,
did you really use a boundary of 24, or 2.4? 2.4 is too small for CG
water (~5 is more reasonable); 24 is too large and would leave a big
vacuum in your initial unit cell.

Peter

Francesco Pietra wrote:
> Hello Axel:
> Indeed I took that into account when devising the procedure, although
> a Boundary of 24 and Box Padding of 15 (12 in a repeated simulation)
> seemed to me to give a gap enough between cells. The analysis was:
>
> molinfo top set a 103
> molinfo top set b 123
> molinfo top set c 93
>
> Graphic Representations ... Periodic... select all x,y,z
>
> Also, I was terrified by the number of water beads already present in
> the above configuration.
>
>
> In answer to Peter also the full set of parameters used for solvation:
> Segment ID Prefix WT
> Boundary 24
> Box size: Use molecule dimensions
> Box padding: 12 throughout
> Use non standard solvent:
> Solvent box pdb: cgwat.pdb
> Solvent box psf: cgwat.psf
> Topology: rbcg-2007.top (added of "Nxg Nxx Nxg 2.988 92 in the Angle sectio)
> Side length: 40 (I did not check this with VMD; with Chimera, more or
> less, it corresponds)
> Key selection: name H2O
>
> Thanks
> francesco
>
>
>
>
> On Tue, Dec 15, 2009 at 9:17 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>
>> On Mon, Dec 14, 2009 at 3:19 AM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
>>
>>> In addition: in agreement with lack of clashes in the system
>>> protein+bilayer, a minimization at const volume of protein_bilayer
>>> (where periodicity and PME were suppressed, otherwise the same conf
>>> input) went to completion, as shown by the final portion of log:
>>>
>> francesco,
>>
>> the obvious conclusion of your description is that
>> you have clashes due to periodicity, i.e. using too
>> small a simulation cell for your system. please keep
>> in mind that coase grained "atoms" are much larger
>> than regular ones and that you thus need a more
>> "safety" distance when computing the size of a cell.
>>
>> cheers,
>> axel.
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
>> Institute for Computational Molecular Science
>> College of Science and Technology
>> Temple University, Philadelphia PA, USA.
>>
>>