Hi everybody,
I have a problem with my molcule.I have protein- ligand complex.One of my
friends works with the same ligand.First of all we use the same mdp files.We
made the simulation.But my calculations were halted.This is the error :
Error on node 1, will try to stop all the nodes
Halting parallel program mdrun_mpi on CPU 1 out of 8
7 additional processes aborted (not shown)
I only can think about the difference may be caused because of my protein
-ligand complex is very big.It has 2 chains.
After that I changed nstcomm ,nstxout ,nstvout ,nstfout, nstlog ,nstenergy,
nstxtcout values than it started to run. But the graphics after the analyze
part(rmsd,gyration...) are very bad.I saw very sharp and meaningless pics.Then
I would like to do the same thing with a paper.In this paper they made the
calculation for 50 ps with position restarint.After they made for 50 ps without
position restraint.At the end they made for 20 ns again full mdp.Idid the
same.But the gyration and rmsd calculations are not the same.Again meaningless
graphics.I have tried to solve the problems for two months.If anything exist to
solve the problems I can send my mdp files.Is there a mistake for my mdp files?
thank you ..
---------------------------------
Need Mail bonding?
Go to the Yahoo! Mail Q&A for great tips from Yahoo! Answers users.
_______________________________________________
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
