Dear friends, I am naive to the Replica exchange Molecular dynamics ( REMD). I have plan to use REMD for temp. 310-320 K to my system. I thoroughly search the Mailing-list Archive for the REMD problem. It was a really helpful to start.
My system consist of peptide + water. I used the following work-flow, Would you please help me to find out my mistakes... 1. energy minimesation for peptide + solvent 2. Different Mdp file for temp. ( 4 temp therefore 4 mdp file ) 3. Make tpr file for each nvt run 4. Then separate equilibration for each temp ( 4 equilibration steps ) 5. Then made NPT.mdp file for each temp ( 4 temp ) 6. Then again equilibration for NPT at 4 temp.( 4 equilibration steps ) 7. Then run md production with -replex 1000 -multi 4 command .. To determine the temp I used web-server http://folding.bmc.uu.se/remd/ Please suggest me any improvements that are possible to implement in my work flow. I will be very grateful to you for your help and suggestion. With Best Regards, Rama David -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists