It works !!! Thank you Justin A bientôt Stefane
ABEL Stephane 175950 wrote: > Hi all, > > I have simulated a system containing 55 DPC molecules, a peptide some ions > and water in a cubic box. Initially all molecules were placed randomly in the > box. As expected during the simulation all the DPC molecules aggregate to > form a stable micelle with the peptide located at the micelle interface. > > Now I would like to plot some MD configs in a PDB format some configs where > the micelle and the peptide are placed in the center of the box. To take into > account the PBC and to obtain the PDB, for the last frame at 150 ns as I used > trjconv with the following commands: > > 1- trjconv_mpi -f traj_KTM17_DPC_all.xtc -s hMRP1_K-TM17_DPC.tpr -pbc nojump > -b 150000 -e 150000 -o traj_KTM17_DPC_0ns_noJump.pdb > > With "non-SOL" (DPC and peptide) as a group for output and where > traj_KTM17_DPC_all.xtc is the trajectory with *no* PBC transformation > > 2- trjconv_mpi -f traj_KTM17_DPC_0ns_noJump.pdb -s hMRP1_K-TM17_dpc.gro > -center -o traj_KTM17_DPC_0ns_noJump_center.pdb > > With DPC as a group for centering and "System" (DPC and peptide) as a group > for output. the *.gro file contains only the DPC and peptide. > > Unfortunately, these commands do not work since the micelle (and the peptide) > are not in the box center. I have tried many others commands with -pbc as > mol, res with no success. > I have never had much success using multi-molecule groups for centering or other correction using trjconv. Centering on the peptide, i.e. trjconv -pbc mol -ur compact -center, should do the trick. I have never found -pbc nojump to work very well, for a reason that is still unknown to me. -Justin > I used GMX version 4.0.7 > > Any advices would be helpful. > > Stefane > > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== ------------------------------ Message: 6 Date: Fri, 20 Aug 2010 13:19:54 -0400 From: "Justin A. Lemkul" <[email protected]> Subject: Re: [gmx-users] intersting problem To: Discussion list for GROMACS users <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset=UTF-8; format=flowed babu gokul wrote: > dear all > I want to calculate the how many water molecule are their with in 3.5 A > of a particular atom. could anyone help me in this regard g_dist -dist -Justin > E R Azhagiya singam > > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== ------------------------------ Message: 7 Date: Fri, 20 Aug 2010 21:55:40 +0200 From: XAvier Periole <[email protected]> Subject: Re: [gmx-users] force constants for umbrellla histograms To: Discussion list for GROMACS users <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes The most important is that you have to put in trajectories that are equilibrated! You can mix as much force constant values you like but always equilibrated ... Then the lower the force constant the longer the simulation needs to be to reach equilibrium: larger conformational space accessible. I can also imagine that a too strong force constant might deform your molecules in a manner you should not. > > Then does it matter how many times you vary it, and how large ? > In my > sampling I have very good histograms up to 2 nm (force constant = 1000 > kj/mol), above 2nm they are not. I feel I may have to use a force > constant of 500 for the next 3 or 4 windows, and even less again > (ca~ 50 > kj/mol) beyond that. > > Cheers > > Gavin > > > XAvier Periole wrote: >> >> On Aug 20, 2010, at 5:12 PM, Gavin Melaugh wrote: >> >>> Hi all >>> >>> Is is O.K to use different force constants for different sampling >>> windows for the generation of the potential of mean force curves? >> Yes. >>> >>> Many Thanks >>> >>> Gavin >>> -- gmx-users mailing list [email protected] >>> http://lists.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 >> > > -- > gmx-users mailing list [email protected] > http://lists.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 ------------------------------ Message: 8 Date: Sat, 21 Aug 2010 11:54:17 +0330 From: leila karami <[email protected]> Subject: [gmx-users] wrong string length 0 for string buf To: gmx-users <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset="iso-8859-1" Hi gromacs users When I uesed command : trjconv -f com_full.xtc -s com_full.tpr -n com.ndx -o com.xtc -pbc nojump -ur compact -center gromacs gives me the following error: Program trjconv, VERSION 4.0.5 Source code file: gmxfio.c, line: 609 Fatal error: wrong string length 0 for string buf (source tpxio.c, line 1641) Any suggestions would be greatly appreciated. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100821/d6c11b84/attachment.html ------------------------------ -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 76, Issue 108 ******************************************
<<winmail.dat>>
-- gmx-users mailing list [email protected] http://lists.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
