[gmx-users] restarting stopped mdrun

- Forwarded Message From: Mohana lakshmi To: gmx-users-requ...@gromacs.org Sent: Mon, 11 July, 2011 1:53:04 PM Subject: restarting stopped mdrun Dear all, I kept mdrun run for 3ns but the job stopped when it reached 1263999 steps due to system shut down. I used tpbconv command

RE: [gmx-users] Fw: g_membed tool

--- On Sun, 20/3/11, Dallas Warren wrote: Dear Dr. Dallas Warren     Thanks for your reply. Could you please tell me in which command should i give the box dimensions   -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Ple

[gmx-users] Fw: g_membed tool

Dear all.. I am using g_membed tools to embed the protein into lipid membrane. I read that before doing g_membed we need to run a short run with some options in .mdp files. what are the steps do we need to do before g_membed. It is given that box size should be taken from the membrane str

[gmx-users] g_membed tool

Dear all.. I am using g_membed tools to embed the protein into lipid membrane. I read that before doing g_membed we need to run a short run with some options in .mdp files. what are the steps do we need to do before g_membed. It is given that box size should be taken from the membrane strucutu

Re: [gmx-users] problem with force fields while running membrane protein simulation

Thank you Mark. Mohanalakshmi N -- gmx-users mailing listgmx-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

Re: [gmx-users] problem with force fields while running membrane protein simulation

Dear Mark I forgot to tell that i could run the same in gromacs older version i.e 3.3.3 but could not run in updated one. I don t know the reason. Please help me. -- Mohanalakshmi N -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] problem with force fields while running membrane protein simulation

Dear all and Justin... I am trying to do membrane protein simulation by following justin's tutorial using gromacs 4.5.3 version. I selected ffG53a6 force field and pasted the content of lipid.itp file to the corresponding files as per the instructions in the tutorial but i got error (Fatal error:

Re: [gmx-users] transmembrane protein simulation

Dear Itamar, > Thank you so much. The website you sent is very useful. > > > > > > Thanks and regards > -- > > > Mohanalakshmi N > > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://

Re: [gmx-users] transmembrane protein simulation

Dear Christopher, > > Thanks for your valuable suggestion. I ll try it. >> >> >> >> Thanks and regards >> -- >> >> >> Mohanalakshmi N >> >> >> -- >> gmx-users mailing listgmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> h

[gmx-users] transmembrane protein simulation

Dear all I am trying to run simulation of transmembrane protein, i am looking for better ways to setup protein with lipid membrane. initially i used VMD to insert protein with lipid membrane but it did not come out well, i got errors while running position restraint. i read about g_membed too

[gmx-users] chcl3 box

hi all.. I need to run simulation in chloroform medium. I have downloaded the .gro and .mdp files for chlroform, but when i run grompp for energy minimization it shows the error "Invalid order for directive atomtypes, file ""chcl3.itp"", line 1" If any one knows please help me Thanks ___

[gmx-users] chloroform box

hi al I need to run simulation in chloroform medium. I have downloaded the .gro and .mdp files for chlroform, but when i run grompp for energy minimization it shows the error "Invalid order for directive atomtypes, file ""chcl3.itp"", line 1" If any one knows please help me Thanks __