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

[Vedat Durmaz]

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.
>>>
>>> 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
>>>
>