[gmx-users] certain number of solvent molecules with genbox WITHOUT "ci"/"nmol" options
durmaz at zib.de
Mon Jan 9 15:18:04 CET 2012
thanks to you two, mark & justin! that's it ...
-maxsol was the keyword for this problem. (which i actually could have
found it myself if having looked carefully after typing "genbox -h")
Am 09.01.2012 13:57, schrieb Mark Abraham:
> On 9/01/2012 11:24 PM, 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.
> Solvating a different initial solute configuration is indeed different
> from attempting an independent replicate :)
> Using -maxsol and a cleverly chosen volume should be able to be made
> work. I've used that for solvating extended and compact versions of
> the same peptide.
>> 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.
>>>> 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" straightening?
>>>> thanks and take care
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