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.
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.
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.
Mark
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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