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. 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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
