[gmx-users] Error in Umbrella sampling command
Dear Sir Presently I am working with the example file as given in the umbrella sampling tutorial. While running the following command grompp -f npt_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx -o npt0.tpr I got the following error. How to debug this error. Ignoring obsolete mdp entry 'title' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5# NOTE 1 [file npt_umbrella.mdp]: nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file npt_umbrella.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 WARNING 1 [file npt_umbrella.mdp]: You are generating velocities so I am assuming you are equilibrating a system. You are using Parrinello-Rahman pressure coupling, but this can be unstable for equilibration. If your system crashes, try equilibrating first with Berendsen pressure coupling. If you are not equilibrating the system, you can probably ignore this warning. ERROR 1 [file npt_umbrella.mdp]: Generating velocities is inconsistent with attempting to continue a previous run. Choose only one of gen-vel = yes and continuation = yes. Generated 165 of the 1596 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_chain_B' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_chain_C' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_chain_D' turning all bonds into constraints... Excluding 3 bonded neighbours molecule type 'Protein_chain_E' turning all bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'NA' turning all bonds into constraints... Excluding 1 bonded neighbours molecule type 'CL' turning all bonds into constraints... Velocities were taken from a Maxwell distribution at 300 K There were 2 notes There was 1 warning --- Program grompp_mpi_d, VERSION 4.6.3 Source code file: /opt/apps/GROMACS/GROMACS-SOURCE/gromacs-4.6.3/src/kernel/gromp p.c, line: 1593 Fatal error: There was 1 error in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I request you to kindly help me to debug the error Regards Arunima -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Conversion of nm to Å
Dear Sir I have to query as to how do we convert the paramaters in nm to Å --. For example the RMSD and RMSF calculation gives result in nm. I want to convert it to Å. I request you to kindly guide me with the process Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] application of MM-GBSA
Hello sir, I require to calculate binding energy using MM-GBSA method. I searched through the manual but i did not find any. i request you to kindly guide to as to which manual to follow to identify binding energy. Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] residue labeling in g_rmsf
Respected Sir If i want my residue name to be labeled in the graph for g_rmsf ,how should I proceed... I used the following command g_rmsf -f md_0_1.xtc -s md_0_1.tpr -res -o rmsf.xvg -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] error in running g_dist
Respected sir I want to calculate the distance between protein and ligand after I have run the production step. I used the following command.. g_dist -s md_0_1.tpr -f md_0_1.xtc -o dist.xvg -n index.ndx Groups I selected was Group 1 (protein) Group 13 (ligand) It says the following error Molecule in topology has atom numbers below and above natoms (11793). You are probably trying to use a trajectory which does not match the first 11793 atoms of the run input file. how to debug the error... -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] residues interaction with ligand
Respected Sir If we have to find the residues surrounding the ligand in protein ligand complex... than which gromacs command should be used... Looking forward for your reply. -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Interaction spectra of inhibitor–residue pair in the protein–inhibitor complexes
Respected sir Which command do we use to determine Interaction spectra of inhibitor–residue pair in the protein–inhibitor complexes as we have g_hbond to determine the hydrogen bond between protein and ligand -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Center of Mass (COM) spacing between protein and ligand
Respected Sir many many thanks for your reply to my last mail. I was able able to debug the error Here I have new set of queries.. How much COM spacing should i consider for my protein-ligand interactiom How much total distance I should move along z-axis/... and which all conf file should i take into consideration for npt_umbrella.mdp... I have my summary_distance.dat as an attachment Here in your example I could not understand as to why have you taken conf0 extending to con450 for ur npt_umbrella.mdp.. I request you to kindly guide me to the next step... -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] system hangs while running perl distances.pl
Respected Sir many many thanks for your reply to my last mail. while running trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep I selected group 0 for the system... but while i run perl distances.pl it says processing file 236...and than the system hangs, no more blinking along the terminal... while when I run indivdual file for distance calculation i am able to run the command g_dist -s pull.tpr -f conf1.gro -n index.ndx -o dist1.xvg groups.txt i request you to kindly guide me to debug the error -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] query respect to perl distances.pl
Respected Sir Presently my work includes umbrella sampling for protein ligand interaction. The components of md_pull.mdp is title = Umbrella pulling simulation define = -DPOSRES_B ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 25; 500 ps nstcomm = 10 ; Output parameters nstxout = 5000 ; every 10 ps nstvout = 5000 nstfout = 500 nstxtcout = 500 ; every 1 ps nstenergy = 500 ; Bond parameters constraint_algorithm= lincs constraints = all-bonds continuation= yes ; continuing from NPT ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb= 1.4 rvdw= 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover tc_grps = Protein Non-Protein tau_t = 0.5 0.5 ref_t = 310 310 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr= EnerPres ; Pull code pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= N N Y pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = Protein pull_group1 = prc pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 where prc is my ligand. ... than I run trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep it generates 500 conf.gro files... but when i run the command perl distances.pl it gives following error atom number 2927 in an index group is larger than number of atoms in the trajectory (2836) which means the trajectory file does not include the ligand component how to overcome this error Regards Arunima -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] groups selection make_ndx -f npt.gro
Hello sir As in the tutorial for umbrella sampling command make_ndx -f npt.gro you have selected two different groups as Chain_A as 19 and Chain_B as 20 If we have protein-ligand interaction whether we should have single group of protein-ligand complex or we should use two different groups for protein and ligand. Regards Arunima -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] error in running distances.pl
Hello Sir While running command for perl distances.pl.. system gets hanged...while processing particular group file... I will be thankful to you if you can guide me in debugging the error -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] error in running perl distance.pl
Hello sir While runnimg command for perl distance.pl in umbrella sampling it gives the following error Use of uninitialized value $distance in concatenation (.) or string at distance.pl line 30. readline() on closed filehandle IN at distance.pl line 16. Can you guide me in rectifying the error -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] center of mass and box co-ordinates
Hello Justin sir In your tutorial file for umbrella sampling for Aβ42 protofibril, what was the criteria used to determine the coordinates of center of mass and box size which you have takes as editconf -f complex.gro -o newbox.gro -center 3.280 2.181 2.4775 -box 6.560 4.362 12 -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Distance of pull group 1 (2.142226 nm) is larger than 0.49 times the box size (2.184750)
Sir I am studying protein-ligand interaction through umbrella sampling. I used the following value foe md_pull.mdp file pull= umbrella pull_geometry = distance ; simple distance increase pull_dim= Y Y Y pull_start = yes ; define initial COM distance 0 pull_ngroups= 1 pull_group0 = Protein pull_group1 = prc pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns pull_k1 = 1000 ; kJ mol^-1 nm^-2 and box size details is editconf -f complex.gro -o newbox.gro -center 3.280 2.181 2.4775 -box 6.560 4.362 12 while runnimg the command for mdrun -s pull.tpr Have the following error Distance of pull group 1 (2.142226 nm) is larger than 0.49 times the box size (2.184750) I request you to kindly help me to debug the error -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] distance of pull group 1 is larger than the box size
Hello sir I got the following error while running pulling mdrun -s pull.tpr distance of pull group 1 is larger than the box size I request you to kindly guide me in overcoming the error -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] PMF calculation between protein and ligand
Sir I have query as to how to go ahead for potential mean force (PMF) calculation between protein and ligand. As per the umbrella sampling protocol you have provided us in gromacs tutotrial it says it is for protein molecules... -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gmx-users Digest, Vol 108, Issue 140
/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! End of gmx-users Digest, Vol 108, Issue 140 *** -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: gmx-users Digest, Vol 109, Issue 2
file.gro -s file.tpr -n waters.ndx -o file1.xpm file2.xpm Error: Internal error in pbc_dx, set pbc has nor been called For more information.. I'm not sure what this means. It seems to be implying that I don't have a box around my polymer, but the gro file clearly shows that my box is 4.94 x 4.94 x 4.94. Any ideas? What is your setting for the pbc keyword in the .mdp file? For g_polystat, I'm a bit worried about the persistence lengths that I get for short polymers. With repeat units smaller than 50 these usually show nan values, that cannot be plotted. From reading the gmx threads I've found that Nan stands for Not a Number, but why do these nan values appear and how can I prevent it so that I can read in my results? This could be an underlying problem related to the above interpretation of periodicity. We don't have enough information to say for sure yet. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Message: 5 Date: Wed, 1 May 2013 01:03:31 + From: Emmanuel, Alaina a.e.emman...@warwick.ac.uk Subject: RE: [gmx-users] help with g_hydorder and g_polystat To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 780d8855cc75c84bb790b79e4e5de7e7269e8...@dbxprd0111mb495.eurprd01.prod.exchangelabs.com Content-Type: text/plain; charset=us-ascii Hello Justin, My mdp file shows that the pbc was set to xyz. Kind Regards, Alaina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 30 April 2013 16:10 To: Discussion list for GROMACS users Subject: Re: [gmx-users] help with g_hydorder and g_polystat On 4/30/13 6:24 AM, Emmanuel, Alaina wrote: Dear All, I'm fairly new to gromacs and having a bit of problem with the g_hydorder and g_polystat. Thanks in advanced for your time. For g_hydorder, I get a fatal error when I type the following command: g_hydorder_d -f file.gro -s file.tpr -n waters.ndx -o file1.xpm file2.xpm Error: Internal error in pbc_dx, set pbc has nor been called For more information.. I'm not sure what this means. It seems to be implying that I don't have a box around my polymer, but the gro file clearly shows that my box is 4.94 x 4.94 x 4.94. Any ideas? What is your setting for the pbc keyword in the .mdp file? For g_polystat, I'm a bit worried about the persistence lengths that I get for short polymers. With repeat units smaller than 50 these usually show nan values, that cannot be plotted. From reading the gmx threads I've found that Nan stands for Not a Number, but why do these nan values appear and how can I prevent it so that I can read in my results? This could be an underlying problem related to the above interpretation of periodicity. We don't have enough information to say for sure yet. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- -- 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! End of gmx-users Digest, Vol 109, Issue 2 * -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive
[gmx-users] Re: gmx-users Digest, Vol 108, Issue 183
-- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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 http://www.gromacs.org/Support/Mailing_Lists -- Message: 6 Date: Tue, 30 Apr 2013 14:03:31 -0500 From: Sikandar Mashayak symasha...@gmail.com Subject: [gmx-users] stable branch using git To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: CAH+j+HLAsr= logz_wrasdnjaaz4twbxhiddiclkpo_sozfy...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Hi I am following the git tutorial for the novice. It says to check out stable version one should use git checkout --track -b release-4-5-patches origin/release-4-5-patches Is there stable branch for 4.6? If yes, how do get it? I tried replacing 4-5 by 4-6 but I get the error: fatal: git checkout: updating paths is incompatible with switching branches. Did you intend to checkout 'origin/release-4-6-patches' which can not be resolved as commit? thanks sikandar -- Message: 7 Date: Tue, 30 Apr 2013 15:10:46 -0400 From: Justin Lemkul jalem...@vt.edu Subject: Re: Aw: [gmx-users] Re: how is the pulling force measured To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 51801736.2080...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 4/30/13 12:33 PM, lloyd riggs wrote: I appologise, I meant defined at the same time without complaining, not just either direction. A different atom order is interpreted as a different interaction. In this case, if both are defined, there is indeed a difference in the improper energy term. I have a toy test case that shows this. -Justin *Gesendet:* Montag, 29. April 2013 um 22:23 Uhr *Von:* lloyd riggs lloyd.ri...@gmx.ch *An:* S. Watkins gmx-users@gromacs.org *Betreff:* Aw: [gmx-users] Re: how is the pulling force measured *Dear All,* *Doing a water/temp energy minimization just for a figure with a large molecule that has several connected parts, I ran into a bizzar question.* *So I found its possible by accident to define improper dihedrails forwards and backwards without gromacs complaining, such as atom 1 2 3 4 and 4 3 2 1. My question is, if your topology has this, does it affect the calculations (angle energy or other)?* *Stephan Watkins* -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- -- 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! End of gmx-users Digest, Vol 108, Issue 183 *** -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] adjust charge
Dear Sir I have query as what criteria do you follow to adjust the charges of ligand atoms in topology file (drg.itp) as you have shown in example for jz4 looking for your reply -- Thanking You with Regards. Arunima Shilpi Ph. D Research Scholar(Cancer Epigenetics) Department of Life Science National Institute of Technology Rourkela Odisha -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] error in running command
Dear Sir/ Madam I am using gromacs for simulation and has the following while running the command for grompp Expected integer argument for option -maxwarn . I do not want use maxwarn to bypass the error. I request you to kindly help me out to debug the error. Regards Arunima -- 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 the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
