[gmx-users] still system exploid

Nicolas Sapay nsapay at ucalgary.ca
Wed Sep 17 19:39:28 CEST 2008

Morteza Khabiri wrote:
> Dear gmxuser,
> Thanks for your all helps. But still I have problem. As you friend said I
> increase the vdw and box size and also i decrease the time step till
> 0.0001 but unfortunately system crash befor EM running. I do check with
> ngmx.
>  To reply the question that said what is your system? My system is ACETONE
> + water + protein  which i mixed water and protein before and i just put
> the protein in the solution of ACETONE and water. 
Are you sure the water+acetone box in which you insert your protein is 
well equilibrated? In my case, I generally make a small box of solvent 
and run a MD simulation of  5-10 ns. Then I solvate my peptides with 
genbox and this small box. Finally, I minimize. When things go really 
wrong like in your case, I remove a thin layer of solvant (~0.3 nm) 
around my peptide, before minimization. I also increase the 
equilibration time in that later case. If you directly use a box the 
size of your protein, you probably have to remove manually overlapping 
solvent molecules before minimization. You may also try to minimize in 2 
steps: 1) minimization of the solvent with restraints on the solute, 2) 
minimization of the whole system.


> About mdp that has a
> popc, I should say that this mdp was fpr my membrane which i used it
> before and i just change some of the parameter of this file and because
> the name was not important i did not change it.
> I am sorry my gro file is big and because of this the gmxmail servic avoid
> to send it. I will send to privet email.
> for coulomb  i use the followings:
>  1-
> coulombtype              = PME
> rcoulomb-switch          = 0
> rcoulomb                 = 1.0
> ; Dielectric constant (DC) for cut-off or DC of reaction field
> epsilon-r                = 1
> ; Method for doing Van der Waals
> vdw-type                 = Cut-off
> ; cut-off lengths
> rvdw-switch              = 0
> rvdw                     = 1.2
> 2-
> coulombtype     = cut-off
> rcoulomb        = 1.8
> vdwtype         = cut-off
> rvdw            = 1.0
> again thanks
> Morteza
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