[gmx-users] certain number of solvent molecules with genbox WITHOUT "ci"/"nmol" options

Vedat Durmaz durmaz at zib.de
Mon Jan 9 13:24:57 CET 2012

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.
> Mark
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.

>> 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
>> vedat

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