[gmx-users] still system exploid

Morteza Khabiri khabiri at greentech.cz
Tue Sep 16 22:58:18 CEST 2008

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
 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. 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:
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

coulombtype     = cut-off
rcoulomb        = 1.8
vdwtype         = cut-off
rvdw            = 1.0

again thanks


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