[gmx-users] How to set a system consists of membranes and cholestrols

Dear gmx_users, Hello, I want to simulate membrane system that contains lipids, cholestrols and glycolipids. Is there any suggestions, advice and some useful links? Best regards, Batsaikhan -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Can I use gromos43a1p-4.5.1.tar.gz in gromacs5.0?

Dear Gmx users, I want to simulate a protein which has phosphorelated residues. Can I use gromos43a1p-4.5.1.tar.gz in gromacs5.0 or 4.6? I have got following error: Program pdb2gmx, VERSION 4.6.5 Source code file: /build/buildd/gromacs-4.6.5/src/kernel/pgutil.c, line: 126 Fatal error: Residue

[gmx-users] How much different run (with posre.itp) from no posre.itp?

Dear gmx-users, I run 3 different conformation of a protein. I run 2 of them no posre.itp and another one has posre.itp. How much different these two run? Sincerely, Batsaikhan -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] How long run should be enough for Free Energy Calculation of a protein?

-extension distance in the mdp file if you are really sure that is the reason. *** Question: Is these calculation reliable? Best regards, Batsaikhan On Sunday, October 19, 2014 2:31 PM, Batdorj Batsaikhan batsaikhan...@yahoo.com wrote: Dear gmx user, please

Re: [gmx-users] How long run should be enough for Free Energy Calculation of a protein?

Dear gmx user, please give me advice about above calculations. Thanks. Batsaikhan On Thursday, October 16, 2014 2:51 PM, Batdorj Batsaikhan batsaikhan...@yahoo.com wrote: I want to calculate free energy of 2 different types of 71 amino acids long protein. I run General Equilibration

[gmx-users] Free energy calculation of

Dear gxm users, Now I am doing solvation free energy of a protein, I follow Sander Pronk's tutorial downloaded from Gromacs page. 1. How do I check system is equilibrated? 2. I run following command sh mklambdas.sh run.mdp topol.top equil.gro I got following error: mklambdas.sh: 12:

[gmx-users] How long run should be enough for Free Energy Calculation of a protein?

Dear gmx-users, Hello, I am working on free energy calculation of a protein. How long run should be enough for Free Energy Calculation of a protein? Batsaikhan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] Can I calculate free energy of Tutorial 1 of Justin's tutorials?

Dear gmx users, Can I calculate free energy of Tutorial 1 of Justin's tutorials? Batsaikhan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Can I simulate heavy atoms in my system?

Dear gmx users, I want to check interaction between heavy atoms (Hg, Pb etc.) and a protein. Can I simulate heavy atoms in our system? Thank you. Best regards, Batsaikhan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

[gmx-users] do_dssp result over written on the one line

Dear gmx users, I done secondary structure analysis using do_dssp. then I converted xpm file to eps. following commands: $ gmx do_dssp -s md3.tpr -f md.xtc -o ss.xpm -tu ns -sss -xvg $ xpm2ps -f ss.xpm -o ss.eps but result of ss.eps is written on the one line. How to fix it? when I open

Re: [gmx-users] do_dssp result over written on the one line

Thank you Justin, It is working but how can I adjust x-axis. My figure y-axis is ok, and x-axis has not time. Best regards, Batsaikhan On Saturday, August 16, 2014 10:00 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/16/14, 7:30 AM, Batdorj Batsaikhan wrote: Dear gmx users, I done

Re: [gmx-users] Can I delete trr file?

Thank you Justin. On Saturday, August 9, 2014 5:40 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/8/14, 10:58 PM, Batdorj Batsaikhan wrote: Dear gmx users, I am new user of gromacs. Our calculations are running, but we have a problem that has not enough disk space. Therefore I need

[gmx-users] Can I delete trr file?

Dear gmx users, I am new user of gromacs. Our calculations are running, but we have a problem that has not enough disk space. Therefore I need to delete some file that are unimportant for analysis. Is there any analysis use trr file? Can I delete trr file? Best regards,  Batsaikhan --

[gmx-users] What files should I delete after simulation?

Dear Users, I have subsequent simulations of MD. I need to delete some unimportant files for analyses. What files should I delete? Best regards,  Batsaikhan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] How to add multiple simulations?

Dear all, I have each of 10 ns five simulations which were subsequently run. How can I join these simulations? Best regards, Batsaikhan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post?

[gmx-users] How can I add subsequent simulations?

Dear all, I have each of 10 ns five simulations which were subsequently run. How can I join these simulations? Best regards, Batsaikhan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post?

[gmx-users] What analysis do I need?

Dear all, I am new user, and I want to analyze conformation change of protein using MD. If you do not mind give me advice. What analysis do I need?  How to use do_dssp? Thank you. Batsaikhan -- Gromacs Users mailing list * Please search the archive at

[gmx-users] How to fix protein went out water?

Dear gmx_users, I am working on simulation of protein in water. 10 ns after the protein went out from water. How to fix this? Can I continue my simulation?  Best regards, Batsaikhan  -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] How to fix protein went out water?

of a periodic system.  All one needs to do is apply trjconv for convenient visualization, and no action needs to be taken to continue the run; mdrun doesn't care about our conventions for watching the trajectory. -Justin Kind regards Thales 2014-06-17 8:56 GMT-03:00 Batdorj Batsaikhan batsaikhan

[gmx-users] How to extend Amber FF parameters of Lipids

Dear gmx users,  I would like to simulate lipid with a protein using AMBER force field. Have you any advice and useful links? Best regards, Batsaikhan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

[gmx-users] How to exit cluster during the simulation

Dear GMX users, I am a new user of gromacs on cluster. I use putty to connect to the cluster. I have a problem. How to exit cluster during the simulation? My last command is mpirun -np 8 mdrun_mpi ...   in the past,  I clicked X button of putty, mdrun did not finished.  Thank you. --

Re: [gmx-users] How to exit cluster during the simulation

Thank you.  Also how to know cpu performance and resting time of simulation after exit. On Sunday, June 15, 2014 12:45 PM, 陈功 gchen...@gmail.com wrote: Seems like :  nohup mpirun -np 8 mdrun_mpi -v -deffnm your_tpr output.info   From: Batdorj Batsaikhan