Morteza Khabiri wrote:
Dear
I make the solution box of organic solvent. It is homeogen and mixed
properly.
It also has a minimum energy. I put one protein in this solution. Before
put the protein in the solution I minimimized it also. Now I mixed 2
system which each of them are minimized. After put the protein in the
solution I try first to minimized it then run it but unfortunately it
crashed. I did not work at all. I also tried to run the system without
minimization but it also did not work at all. I changed mdp file (
If the system crashes during minimization, I certainly wouldn't expect it to do
anything but crash if you don't run EM!
eg,remove center of mass motion or decrease the temprature,..) but non of
them did work.
Usually it is better to show the .mdp file than to make us guess at what you've
got...
Thats very nice of you if you guid me what should i do?
Dealing with mixed solvents can be difficult. You probably have some severe
overlap that cannot be resolved by energy minimization. Usually if you set
nstxout = 1 in the .mdp file you can get a glimpse of where the system begins to
explode. That will provide some clues.
-Justin
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
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
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
