[gmx-users] certain number of solvent molecules with genbox WITHOUT "ci"/"nmol" options
Justin A. Lemkul
jalemkul at vt.edu
Mon Jan 9 13:54:02 CET 2012
Vedat Durmaz wrote:
> Am 09.01.2012 12:37, schrieb Mark Abraham:
>> On 9/01/2012 9:00 PM, Vedat Durmaz wrote:
>>> hi guys,
>>> i have a molecular system that i want to simulate many times with
>>> differing initial conditions, but each with the same number of
>>> (solvent) atoms! i'm using gromacs 4.5.4 ...
>> Use different values for gen_seed. By the time you equilibrate the
>> positional correlations will be lost.
> thanks for your help, mark. but you didn't get the point. let me try to
> describe it again:
> the positions of the solvent atoms are not important. i just need the
> same number of solvent molecules within any of the 50 systems. the
> differences of these systems are already given by different
> conformations of the ligand.
> as written below, genbox -cs doesn't yield in the same number of solvent
> molecules for the 50 occurrences of the same system. in contrast,
> "genbox -ci ... -nmol 23000" would result in the same number of solvent
> molecules, however it runs into the error "Cannot allocate memory"
> having reached memory limit (which has 40 GB size!).
> what i would like to know is whether there is a way of telling genbox to
> put a certain number of solvent molecules without using the -ci option
> (which requires more memory than my system offers).
> if there is no other way, i will have to change each of the 50
> topologies and pdb files manually in order to keep an equal number of
> solvent molecules for each system.
Use the -maxsol option to limit the number of water molecules to some specified
value. In conjunction with the normal -cs, the program is limited to whatever
value you specify.
>>> genbox with "-cs" gives me different numbers of solvent molecules.
>>> putting more than 20,000 tip4p molecules with the "-ci" and "-nmol"
>>> combination of genbox instead runs into memory problems (40 GB is not
>>> sufficient for one single system!).
>>> does anyone know another way of solving that issue avoiding "manual"
>>> thanks and take care
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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