Re: [gmx-users] Calculating shear viscosity of a liquid - different results from different verions of Gromacs
Hi, There are some known issues fixed in 4.6 ( http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x) but since the authors of this code haven't added any test cases, AFAIK it could have gotten broken at any time. I can't see any obvious .mdp issues. I would encourage you to attempt to replicate the original work, and see what that tells you. Mark On Fri, Dec 18, 2015 at 3:33 AM Mateusz Jasik wrote: > Dear Gromacs Users, > > I am trying to obtain the shear viscosity of an imidazolium-based ionic > liquid by using periodic perturbation method. While recalculating some of > mine old data, it turned out, that the results I get from the Gromacs 4.6.7 > are different from those obtained from Gromacs 4.5.5 by two orders of > magnitude. > > As a test I have run a calculations using the same tpr files (created by > the 4.5.5 verison) and two versions of gromacs. The mdp file I used is > presented below: > > title = nvT MD > integrator = md > constraints = all-bonds > dt = 0.001 > nsteps = 1200 > nstenergy = 100 > nstlist = 10 > nstxout = 0 > nstvout = 0 > nstfout = 0 > nstlog = 100 > nstxtcout = 1000 > xtcprecision= 1000 > ns_type = grid > coulombtype = PME > rlist = 1.0 > rcoulomb= 1.0 > rvdw= 1.0 > tcoupl = nose-hoover > tc_grps = MENIM Tf2N > tau_t = 0.1 0.1 > ref_t = 303.15 303.15 > Pcoupl = No > gen_vel = no > gen_temp= 298 > gen_seed= 173529 > energygrps = MENIM Tf2N > constraint_algorithm = LINCS > pbc = xyz > cos_acceleration= 0.01; I have run simulations for five > different values, ranging from 0.01 to 0.05 > > > I obtained the 1/Viscosity values using "g_energy -f edr_file -s tpr_file > -o output.xvg". > > Here are the values I got from the program: > > cos_acceleration1/Viscosity (4.5.5)1/Viscosity (4.6.7) > 0.01 0.0583586 > 5,91038 > 0.02 0.3713 > 57,4981 > 0.03 1.24583 > 211.699 > 0.04 2.73402 > 475.518 > 0.05 4.02399 > 807.279 > > There have previously been numerous threads regarding the viscosity > calculations, but I haven't found any with the problem similar to this. Are > there any differences between the two version of program that can influence > this value? And if so, which one should I treat as the more reliable? Or > could this be a problem from my side (for example with the parameters used)? > > Thanks and regards, > Mateusz > > -- > 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 > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] gromacs with v-rescale thermostat
Hi, Indeed, we changed this behaviour for 5.0 (and noted it at http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x) Mark On Sat, Dec 19, 2015 at 1:00 AM wrote: > Dear users, > recently I have observed a strange behavior of my simulations. The total > potential energy of presumably independent simulations showed undesired > correlation (R=0.6) even when started with different velocities > (gen-seed=-1) and solute coordinates. > > I found out that the reason is the v-rescale thermostat, which uses random > numbers seeded by the ld-seed option in the mdp file. Unfortunately in > gromacs 4.5 and 4.6 series, the default value is 1993, which causes the > interdependence of the trajectories. > > The solution is to explicitly set ld-seed = -1 everytime the v-rescale > thermostat is used. This is also the default value in gromacs 5+ versions. > > Hope this helps. > > > with best regards > > > Michal > > > > > -- > 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 > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Help calculation on cluster
Try: echo "0" | g_mmpbsa -f traj.xtc -s topol.tpr -i mmpbsa.mdp -n index.ndx -nomme -pbsa -nodecomp -apol apolar.xvg -nodiff In your submission file. Where "0" is the index number of the group you are interested in. === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mishelle Oña Sent: Friday, December 18, 2015 3:04 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Help calculation on cluster Thanks for your reply Micholas, I ask my system admins but he told me that for queuing the job I need to enter the selected group in the command line. My command is g_mmpbsa -f traj.xtc -s topol.tpr -i mmpbsa.mdp -n index.ndx -nomme -pbsa -nodecomp -apol apolar.xvg -nodiff My question was if I can add something to this command in order to select the atom group I wanted to use instead of selecting it from the group list that appears after the job is submitted? Mishelle > From: smit...@ornl.gov > To: gmx-us...@gromacs.org > Date: Fri, 18 Dec 2015 19:47:22 + > Subject: Re: [gmx-users] Help calculation on cluster > > Not really the best place to ask this question (check with your system > admins), but > > You could run your command from a "screen session". > > Just run screen when you first log into the machine, go about your business > setting up your simulation and then start it. Once it is running, type > control-a-d to detach from the session. It will continue to run until > completion, or the computer crashes, whether you close the terminal or not. > And you can always re-attach to the screen session to see what is going on > from a new terminal if you need to. > > Ideally, though, you would just submit your job to a queuing system and wait > for it to finish...be sure to check with your sys. admins. > > > === > Micholas Dean Smith, PhD. > Post-doctoral Research Associate > University of Tennessee/Oak Ridge National Laboratory > Center for Molecular Biophysics > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Mishelle Oña > > Sent: Friday, December 18, 2015 2:40 PM > To: gmx-us...@gromacs.org > Subject: [gmx-users] Help calculation on cluster > > Hi, > I am doing some simulations in a cluster. I want to know if there is an > option to run the simulation in order that I can close the terminal?. I tried > to make sbatch but the problem is that when I entered the command there is a > step to choose the system and with sbatch I could not choose this option. > Thank youMishelle > -- > 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 > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. > > -- > 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 > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PCA analysis results
Hi Nithyanan, It's guessing a bit, as the actual answer can only be obtained by tracking some parameters during the simulation, but I would suggest to aim for at least 200 ns. It think the relaxation will take more time than you have, so say until (at least) 100 ns, and then you need to have enough sampling to characterize the dynamics after relaxation. Cheers, Tsjerk On Fri, Dec 18, 2015 at 9:14 PM, Nithyanan Annamalai wrote: > Dr Tsjerk, > > Thank you for your explanation. > > The PDB model I used in this simulation was obtained from I-TASSER. > There is no ligand involved. > > Dr, may I know what would be the optimal/ suggested simulation time for > this protein with 567 aa? > > On Sat, Dec 19, 2015 at 4:06 AM, Tsjerk Wassenaar > wrote: > > > Hi Nithyanan, > > > > Right. So now we have that clear, I've had a look at the PDB file :p > > What you see is the result of filtering over a single eigenvector. You > > protein is kind of curling up through rotations of domains. You can't > > describe these rotations with a single eigenvector. They will be > dispersed > > over multiple, and you will need at least two to capture the rotations. > > Maybe there's a twist associated and then you'd surely need one more. > > > > As an aside, looking at the trajectory confirms me that this is a > > relaxation motion. I don't know whether you removed a ligand and this is > a > > functional relaxation, or that is was started from a crystal structure, > but > > it is something to be aware of. > > > > Hope it helps, > > > > Tsjerk > > > > On Fri, Dec 18, 2015 at 8:51 PM, Nithyanan Annamalai < > > nithyann...@gmail.com> > > wrote: > > > > > Hi Dr Tsjerk, > > > > > > I didn't do any clustering or make it whole. > > > > > > I just use the .xtc that I ontained after the simulation since I found > > out > > > there is no pbc effect of the protein. > > > > > > On Sat, Dec 19, 2015 at 3:42 AM, Tsjerk Wassenaar > > > wrote: > > > > > > > Hi Nithyanan, > > > > > > > > How did you preprocess the trajectory? Did you cluster and/or make > > > > everything whole? > > > > > > > > By the way, 50 ns is probably too short for a protein of that size. > It > > > will > > > > probably still be relaxing and the eigenvectors will be those of the > > > > relaxation. > > > > > > > > Cheers, > > > > > > > > Tsjerk > > > > > > > > On Fri, Dec 18, 2015 at 8:34 PM, Nithyanan Annamalai < > > > > nithyann...@gmail.com> > > > > wrote: > > > > > > > > > Dear GROMACS users, > > > > > > > > > > I have performed 50ns MD for 567 aa monomer protein using > gromos53a6 > > ff > > > > in > > > > > explicit water in the cubic box with 2fs time step. > > > > > > > > > > I have used g_covar and g_anaeig to perform Principal Component > > > > Analysis/ > > > > > Essential Dynamics analysis. > > > > > > > > > > > > > > > But when I view the animation of the trajectory it, the movement of > > the > > > > > protein looks weird. > > > > > > > > > > Can anyone please help to explain to me what I can do to get the > > right > > > > > trajectory? > > > > > > > > > > Link for eigenvalue file: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > https://drive.google.com/file/d/0B2PnnS1LZvokVS10N0dDTXFWRGM/view?usp=sharing > > > > > > > > > > I have used the following command line to extract the results: > > > > > > > > > > > > > > > g_anaeig -f ../../md_0_1.xtc -s ../../md_0_1.tpr -n ../../index.ndx > > -v > > > > > ../../phac_monomer_50ns_wild_Protein_eigenvec.trr -eig > > > > > ../../phac_monomer_50ns_wild_Protein_eigenval.xvg -filt > > > > mono_wild_filt1.pdb > > > > > -rmsf mono_wild_PC1_eigrmsf.xvg -first 1 -last 1 -skip 100 > > > > > > > > > > pdb file link: > > > > > > > > > > > > > > > > > > > > > > > > > https://drive.google.com/file/d/0B2PnnS1LZvokbzdqN1VvVWtxUU0/view?usp=sharing > > > > > > > > > > g_anaeig -f ../../md_0_1.xtc -s ../../md_0_1.tpr -n > ../../index.ndx > > -v > > > > > ../../phac_monomer_50ns_wild_Protein_eigenvec.trr -eig > > > > > ../../phac_monomer_50ns_wild_Protein_eigenval.xvg -extr > > > > > mono_wild_extreme1.pdb -first 1 -last 1 -nframes 50 > > > > > > > > > > pdb file link: > > > > > > > > > > > > > > > > > > > > https://drive.google.com/file/d/0B2PnnS1LZvokSE5OMUZLbGl4MDA/view?usp=sharing > > > > > -- > > > > > 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 > > > > > > > > > > * For (un)subscribe requests visit > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > or > > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > > > > > > > > > > > > > > > -- > > > > Tsjerk A. Wassenaar, Ph.D. > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > posting! > > > >
Re: [gmx-users] PCA analysis results
Dr Tsjerk, Thank you for your explanation. The PDB model I used in this simulation was obtained from I-TASSER. There is no ligand involved. Dr, may I know what would be the optimal/ suggested simulation time for this protein with 567 aa? On Sat, Dec 19, 2015 at 4:06 AM, Tsjerk Wassenaar wrote: > Hi Nithyanan, > > Right. So now we have that clear, I've had a look at the PDB file :p > What you see is the result of filtering over a single eigenvector. You > protein is kind of curling up through rotations of domains. You can't > describe these rotations with a single eigenvector. They will be dispersed > over multiple, and you will need at least two to capture the rotations. > Maybe there's a twist associated and then you'd surely need one more. > > As an aside, looking at the trajectory confirms me that this is a > relaxation motion. I don't know whether you removed a ligand and this is a > functional relaxation, or that is was started from a crystal structure, but > it is something to be aware of. > > Hope it helps, > > Tsjerk > > On Fri, Dec 18, 2015 at 8:51 PM, Nithyanan Annamalai < > nithyann...@gmail.com> > wrote: > > > Hi Dr Tsjerk, > > > > I didn't do any clustering or make it whole. > > > > I just use the .xtc that I ontained after the simulation since I found > out > > there is no pbc effect of the protein. > > > > On Sat, Dec 19, 2015 at 3:42 AM, Tsjerk Wassenaar > > wrote: > > > > > Hi Nithyanan, > > > > > > How did you preprocess the trajectory? Did you cluster and/or make > > > everything whole? > > > > > > By the way, 50 ns is probably too short for a protein of that size. It > > will > > > probably still be relaxing and the eigenvectors will be those of the > > > relaxation. > > > > > > Cheers, > > > > > > Tsjerk > > > > > > On Fri, Dec 18, 2015 at 8:34 PM, Nithyanan Annamalai < > > > nithyann...@gmail.com> > > > wrote: > > > > > > > Dear GROMACS users, > > > > > > > > I have performed 50ns MD for 567 aa monomer protein using gromos53a6 > ff > > > in > > > > explicit water in the cubic box with 2fs time step. > > > > > > > > I have used g_covar and g_anaeig to perform Principal Component > > > Analysis/ > > > > Essential Dynamics analysis. > > > > > > > > > > > > But when I view the animation of the trajectory it, the movement of > the > > > > protein looks weird. > > > > > > > > Can anyone please help to explain to me what I can do to get the > right > > > > trajectory? > > > > > > > > Link for eigenvalue file: > > > > > > > > > > > > > > > > > > > > > > https://drive.google.com/file/d/0B2PnnS1LZvokVS10N0dDTXFWRGM/view?usp=sharing > > > > > > > > I have used the following command line to extract the results: > > > > > > > > > > > > g_anaeig -f ../../md_0_1.xtc -s ../../md_0_1.tpr -n ../../index.ndx > -v > > > > ../../phac_monomer_50ns_wild_Protein_eigenvec.trr -eig > > > > ../../phac_monomer_50ns_wild_Protein_eigenval.xvg -filt > > > mono_wild_filt1.pdb > > > > -rmsf mono_wild_PC1_eigrmsf.xvg -first 1 -last 1 -skip 100 > > > > > > > > pdb file link: > > > > > > > > > > > > > > > > > > https://drive.google.com/file/d/0B2PnnS1LZvokbzdqN1VvVWtxUU0/view?usp=sharing > > > > > > > > g_anaeig -f ../../md_0_1.xtc -s ../../md_0_1.tpr -n ../../index.ndx > -v > > > > ../../phac_monomer_50ns_wild_Protein_eigenvec.trr -eig > > > > ../../phac_monomer_50ns_wild_Protein_eigenval.xvg -extr > > > > mono_wild_extreme1.pdb -first 1 -last 1 -nframes 50 > > > > > > > > pdb file link: > > > > > > > > > > > > > > https://drive.google.com/file/d/0B2PnnS1LZvokSE5OMUZLbGl4MDA/view?usp=sharing > > > > -- > > > > 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 > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > > > > > > > > > > -- > > > Tsjerk A. Wassenaar, Ph.D. > > > -- > > > 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 > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > 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 > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > Gromacs Users mailing list > > * Please search
Re: [gmx-users] PCA analysis results
Hi Nithyanan, Right. So now we have that clear, I've had a look at the PDB file :p What you see is the result of filtering over a single eigenvector. You protein is kind of curling up through rotations of domains. You can't describe these rotations with a single eigenvector. They will be dispersed over multiple, and you will need at least two to capture the rotations. Maybe there's a twist associated and then you'd surely need one more. As an aside, looking at the trajectory confirms me that this is a relaxation motion. I don't know whether you removed a ligand and this is a functional relaxation, or that is was started from a crystal structure, but it is something to be aware of. Hope it helps, Tsjerk On Fri, Dec 18, 2015 at 8:51 PM, Nithyanan Annamalai wrote: > Hi Dr Tsjerk, > > I didn't do any clustering or make it whole. > > I just use the .xtc that I ontained after the simulation since I found out > there is no pbc effect of the protein. > > On Sat, Dec 19, 2015 at 3:42 AM, Tsjerk Wassenaar > wrote: > > > Hi Nithyanan, > > > > How did you preprocess the trajectory? Did you cluster and/or make > > everything whole? > > > > By the way, 50 ns is probably too short for a protein of that size. It > will > > probably still be relaxing and the eigenvectors will be those of the > > relaxation. > > > > Cheers, > > > > Tsjerk > > > > On Fri, Dec 18, 2015 at 8:34 PM, Nithyanan Annamalai < > > nithyann...@gmail.com> > > wrote: > > > > > Dear GROMACS users, > > > > > > I have performed 50ns MD for 567 aa monomer protein using gromos53a6 ff > > in > > > explicit water in the cubic box with 2fs time step. > > > > > > I have used g_covar and g_anaeig to perform Principal Component > > Analysis/ > > > Essential Dynamics analysis. > > > > > > > > > But when I view the animation of the trajectory it, the movement of the > > > protein looks weird. > > > > > > Can anyone please help to explain to me what I can do to get the right > > > trajectory? > > > > > > Link for eigenvalue file: > > > > > > > > > > > > > > > https://drive.google.com/file/d/0B2PnnS1LZvokVS10N0dDTXFWRGM/view?usp=sharing > > > > > > I have used the following command line to extract the results: > > > > > > > > > g_anaeig -f ../../md_0_1.xtc -s ../../md_0_1.tpr -n ../../index.ndx -v > > > ../../phac_monomer_50ns_wild_Protein_eigenvec.trr -eig > > > ../../phac_monomer_50ns_wild_Protein_eigenval.xvg -filt > > mono_wild_filt1.pdb > > > -rmsf mono_wild_PC1_eigrmsf.xvg -first 1 -last 1 -skip 100 > > > > > > pdb file link: > > > > > > > > > > > > https://drive.google.com/file/d/0B2PnnS1LZvokbzdqN1VvVWtxUU0/view?usp=sharing > > > > > > g_anaeig -f ../../md_0_1.xtc -s ../../md_0_1.tpr -n ../../index.ndx -v > > > ../../phac_monomer_50ns_wild_Protein_eigenvec.trr -eig > > > ../../phac_monomer_50ns_wild_Protein_eigenval.xvg -extr > > > mono_wild_extreme1.pdb -first 1 -last 1 -nframes 50 > > > > > > pdb file link: > > > > > > > > > https://drive.google.com/file/d/0B2PnnS1LZvokSE5OMUZLbGl4MDA/view?usp=sharing > > > -- > > > 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 > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > > > > > -- > > Tsjerk A. Wassenaar, Ph.D. > > -- > > 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 > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > 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 > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Tsjerk A. Wassenaar, Ph.D. -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Help calculation on cluster
Thanks for your reply Micholas, I ask my system admins but he told me that for queuing the job I need to enter the selected group in the command line. My command is g_mmpbsa -f traj.xtc -s topol.tpr -i mmpbsa.mdp -n index.ndx -nomme -pbsa -nodecomp -apol apolar.xvg -nodiff My question was if I can add something to this command in order to select the atom group I wanted to use instead of selecting it from the group list that appears after the job is submitted? Mishelle > From: smit...@ornl.gov > To: gmx-us...@gromacs.org > Date: Fri, 18 Dec 2015 19:47:22 + > Subject: Re: [gmx-users] Help calculation on cluster > > Not really the best place to ask this question (check with your system > admins), but > > You could run your command from a "screen session". > > Just run screen when you first log into the machine, go about your business > setting up your simulation and then start it. Once it is running, type > control-a-d to detach from the session. It will continue to run until > completion, or the computer crashes, whether you close the terminal or not. > And you can always re-attach to the screen session to see what is going on > from a new terminal if you need to. > > Ideally, though, you would just submit your job to a queuing system and wait > for it to finish...be sure to check with your sys. admins. > > > === > Micholas Dean Smith, PhD. > Post-doctoral Research Associate > University of Tennessee/Oak Ridge National Laboratory > Center for Molecular Biophysics > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Mishelle Oña > > Sent: Friday, December 18, 2015 2:40 PM > To: gmx-us...@gromacs.org > Subject: [gmx-users] Help calculation on cluster > > Hi, > I am doing some simulations in a cluster. I want to know if there is an > option to run the simulation in order that I can close the terminal?. I tried > to make sbatch but the problem is that when I entered the command there is a > step to choose the system and with sbatch I could not choose this option. > Thank youMishelle > -- > 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 > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. > > -- > 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 > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PCA analysis results
Hi Dr Tsjerk, I didn't do any clustering or make it whole. I just use the .xtc that I ontained after the simulation since I found out there is no pbc effect of the protein. On Sat, Dec 19, 2015 at 3:42 AM, Tsjerk Wassenaar wrote: > Hi Nithyanan, > > How did you preprocess the trajectory? Did you cluster and/or make > everything whole? > > By the way, 50 ns is probably too short for a protein of that size. It will > probably still be relaxing and the eigenvectors will be those of the > relaxation. > > Cheers, > > Tsjerk > > On Fri, Dec 18, 2015 at 8:34 PM, Nithyanan Annamalai < > nithyann...@gmail.com> > wrote: > > > Dear GROMACS users, > > > > I have performed 50ns MD for 567 aa monomer protein using gromos53a6 ff > in > > explicit water in the cubic box with 2fs time step. > > > > I have used g_covar and g_anaeig to perform Principal Component > Analysis/ > > Essential Dynamics analysis. > > > > > > But when I view the animation of the trajectory it, the movement of the > > protein looks weird. > > > > Can anyone please help to explain to me what I can do to get the right > > trajectory? > > > > Link for eigenvalue file: > > > > > > > > > https://drive.google.com/file/d/0B2PnnS1LZvokVS10N0dDTXFWRGM/view?usp=sharing > > > > I have used the following command line to extract the results: > > > > > > g_anaeig -f ../../md_0_1.xtc -s ../../md_0_1.tpr -n ../../index.ndx -v > > ../../phac_monomer_50ns_wild_Protein_eigenvec.trr -eig > > ../../phac_monomer_50ns_wild_Protein_eigenval.xvg -filt > mono_wild_filt1.pdb > > -rmsf mono_wild_PC1_eigrmsf.xvg -first 1 -last 1 -skip 100 > > > > pdb file link: > > > > > > > https://drive.google.com/file/d/0B2PnnS1LZvokbzdqN1VvVWtxUU0/view?usp=sharing > > > > g_anaeig -f ../../md_0_1.xtc -s ../../md_0_1.tpr -n ../../index.ndx -v > > ../../phac_monomer_50ns_wild_Protein_eigenvec.trr -eig > > ../../phac_monomer_50ns_wild_Protein_eigenval.xvg -extr > > mono_wild_extreme1.pdb -first 1 -last 1 -nframes 50 > > > > pdb file link: > > > > > https://drive.google.com/file/d/0B2PnnS1LZvokSE5OMUZLbGl4MDA/view?usp=sharing > > -- > > 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 > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > 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 > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Help calculation on cluster
Not really the best place to ask this question (check with your system admins), but You could run your command from a "screen session". Just run screen when you first log into the machine, go about your business setting up your simulation and then start it. Once it is running, type control-a-d to detach from the session. It will continue to run until completion, or the computer crashes, whether you close the terminal or not. And you can always re-attach to the screen session to see what is going on from a new terminal if you need to. Ideally, though, you would just submit your job to a queuing system and wait for it to finish...be sure to check with your sys. admins. === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mishelle Oña Sent: Friday, December 18, 2015 2:40 PM To: gmx-us...@gromacs.org Subject: [gmx-users] Help calculation on cluster Hi, I am doing some simulations in a cluster. I want to know if there is an option to run the simulation in order that I can close the terminal?. I tried to make sbatch but the problem is that when I entered the command there is a step to choose the system and with sbatch I could not choose this option. Thank youMishelle -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Help calculation on cluster
On 12/18/15 2:40 PM, Mishelle Oña wrote: Hi, I am doing some simulations in a cluster. I want to know if there is an option to run the simulation in order that I can close the terminal?. I tried to make sbatch but the problem is that when I entered the command there is a step to choose the system and with sbatch I could not choose this option. http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts For specific usage of your cluster, talk to your sysadmin. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PCA analysis results
Hi Nithyanan, How did you preprocess the trajectory? Did you cluster and/or make everything whole? By the way, 50 ns is probably too short for a protein of that size. It will probably still be relaxing and the eigenvectors will be those of the relaxation. Cheers, Tsjerk On Fri, Dec 18, 2015 at 8:34 PM, Nithyanan Annamalai wrote: > Dear GROMACS users, > > I have performed 50ns MD for 567 aa monomer protein using gromos53a6 ff in > explicit water in the cubic box with 2fs time step. > > I have used g_covar and g_anaeig to perform Principal Component Analysis/ > Essential Dynamics analysis. > > > But when I view the animation of the trajectory it, the movement of the > protein looks weird. > > Can anyone please help to explain to me what I can do to get the right > trajectory? > > Link for eigenvalue file: > > > > https://drive.google.com/file/d/0B2PnnS1LZvokVS10N0dDTXFWRGM/view?usp=sharing > > I have used the following command line to extract the results: > > > g_anaeig -f ../../md_0_1.xtc -s ../../md_0_1.tpr -n ../../index.ndx -v > ../../phac_monomer_50ns_wild_Protein_eigenvec.trr -eig > ../../phac_monomer_50ns_wild_Protein_eigenval.xvg -filt mono_wild_filt1.pdb > -rmsf mono_wild_PC1_eigrmsf.xvg -first 1 -last 1 -skip 100 > > pdb file link: > > > https://drive.google.com/file/d/0B2PnnS1LZvokbzdqN1VvVWtxUU0/view?usp=sharing > > g_anaeig -f ../../md_0_1.xtc -s ../../md_0_1.tpr -n ../../index.ndx -v > ../../phac_monomer_50ns_wild_Protein_eigenvec.trr -eig > ../../phac_monomer_50ns_wild_Protein_eigenval.xvg -extr > mono_wild_extreme1.pdb -first 1 -last 1 -nframes 50 > > pdb file link: > > https://drive.google.com/file/d/0B2PnnS1LZvokSE5OMUZLbGl4MDA/view?usp=sharing > -- > 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 > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Tsjerk A. Wassenaar, Ph.D. -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Help calculation on cluster
Hi, I am doing some simulations in a cluster. I want to know if there is an option to run the simulation in order that I can close the terminal?. I tried to make sbatch but the problem is that when I entered the command there is a step to choose the system and with sbatch I could not choose this option. Thank youMishelle -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PCA analysis results
Dear GROMACS users, I have performed 50ns MD for 567 aa monomer protein using gromos53a6 ff in explicit water in the cubic box with 2fs time step. I have used g_covar and g_anaeig to perform Principal Component Analysis/ Essential Dynamics analysis. But when I view the animation of the trajectory it, the movement of the protein looks weird. Can anyone please help to explain to me what I can do to get the right trajectory? Link for eigenvalue file: https://drive.google.com/file/d/0B2PnnS1LZvokVS10N0dDTXFWRGM/view?usp=sharing I have used the following command line to extract the results: g_anaeig -f ../../md_0_1.xtc -s ../../md_0_1.tpr -n ../../index.ndx -v ../../phac_monomer_50ns_wild_Protein_eigenvec.trr -eig ../../phac_monomer_50ns_wild_Protein_eigenval.xvg -filt mono_wild_filt1.pdb -rmsf mono_wild_PC1_eigrmsf.xvg -first 1 -last 1 -skip 100 pdb file link: https://drive.google.com/file/d/0B2PnnS1LZvokbzdqN1VvVWtxUU0/view?usp=sharing g_anaeig -f ../../md_0_1.xtc -s ../../md_0_1.tpr -n ../../index.ndx -v ../../phac_monomer_50ns_wild_Protein_eigenvec.trr -eig ../../phac_monomer_50ns_wild_Protein_eigenval.xvg -extr mono_wild_extreme1.pdb -first 1 -last 1 -nframes 50 pdb file link: https://drive.google.com/file/d/0B2PnnS1LZvokSE5OMUZLbGl4MDA/view?usp=sharing -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] POVPC MARTINI ff
Try again =) On 17 December 2015 at 16:17, shivangi nangia wrote: > Hello, > > Thanks for your reply. > > That weblink, however, is not working. > > Is there somewhere else I can look. > > CHARMM GUI MARTINI membrane builder also does not have POVPC MARTINI ff. > > Thanks, > sxn > > > > > > On Thu, Dec 17, 2015 at 4:43 AM, Catarina A. Carvalheda dos Santos < > c.a.c.dossan...@dundee.ac.uk> wrote: > > > Hi Shivangi, > > > > Check the Lipidbook @ http://lipidbook.bioch.ox.ac.uk > > > > Cheers, > > > > On 17 December 2015 at 04:14, shivangi nangia > > > wrote: > > > > > Hello All, > > > > > > I am looking for MARTINI ff for POVPC, its not on MARTNI webpage. > > > > > > It will be great if anyone can help me with it. > > > > > > Thanks in advance. > > > > > > Regards, > > > sxn > > > -- > > > 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 > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > The University of Dundee is a registered Scottish Charity, No: SC015096 > > > > > > > > > > > -- > > Catarina A. Carvalheda > > > > PhD Student > > Computational Biology Division > > SSE & SLS > > University of Dundee > > DD1 5EH, Dundee, Scotland, UK > > -- > > 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 > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > 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 > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > The University of Dundee is a registered Scottish Charity, No: SC015096 > -- Catarina A. Carvalheda PhD Student Computational Biology Division SSE & SLS University of Dundee DD1 5EH, Dundee, Scotland, UK -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Simulations of inorganic polymers
On 12/18/15 8:47 AM, Ganesh Shahane wrote: Dear Gromacs Users, I need to simulate a specific polymer which consists of carbon, hydrogen and fluorine atoms. Could anyone please suggest some force fields for simulating inorganic polymer molecules that have been ported to gromacs? Your polymer is organic since it has carbon. Most force fields in GROMACS should, in principle, support such species, but you need to do a literature search on your own to figure out the best available options that other investigators have used for similar systems. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] regarding the use of g_hbond
On 12/18/15 5:42 AM, soumadwip ghosh wrote: Hi all, I am trying to plot the no.of hydrogen bonds between two parallel chains of a double stranded DNA as a function of time. What I am observing is a decrease (which is expected) for two types of nucleic acids but the problem is the difference between three or more data are difficult to visualize due to large data points. I want the plot to look something like FIG 6 of the following reference below http://scitation.aip.org/docserver/fulltext/aip/journal/jcp/136/6/1.3682780.pdf?expires=1450435942&id=id&accname=2102180&checksum=AC45165AFD6BC0C361795C50AED25E13 This link is broken. where the difference is clearly observed. However what I am getting from GROMACS 5.0.5 and Origin software is something as follows https://drive.google.com/file/d/0B7SBnQ5YXQSLYUxiSk9aRVIwbzg/view?usp=sharing Is there any workaround to achieve what I am looking for? Your data seem pretty clear as they are. Perhaps try plotting as a running average to remove some of the fluctuation. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] gromacs with v-rescale thermostat
Dear users, recently I have observed a strange behavior of my simulations. The total potential energy of presumably independent simulations showed undesired correlation (R=0.6) even when started with different velocities (gen-seed=-1) and solute coordinates. I found out that the reason is the v-rescale thermostat, which uses random numbers seeded by the ld-seed option in the mdp file. Unfortunately in gromacs 4.5 and 4.6 series, the default value is 1993, which causes the interdependence of the trajectories. The solution is to explicitly set ld-seed = -1 everytime the v-rescale thermostat is used. This is also the default value in gromacs 5+ versions. Hope this helps. with best regards Michal -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Simulations of inorganic polymers
Dear Gromacs Users, I need to simulate a specific polymer which consists of carbon, hydrogen and fluorine atoms. Could anyone please suggest some force fields for simulating inorganic polymer molecules that have been ported to gromacs? Thank you. -- Best Regards, Ganesh Shahane -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] regarding the use of g_hbond
Hi all, I am trying to plot the no.of hydrogen bonds between two parallel chains of a double stranded DNA as a function of time. What I am observing is a decrease (which is expected) for two types of nucleic acids but the problem is the difference between three or more data are difficult to visualize due to large data points. I want the plot to look something like FIG 6 of the following reference below http://scitation.aip.org/docserver/fulltext/aip/journal/jcp/136/6/1.3682780.pdf?expires=1450435942&id=id&accname=2102180&checksum=AC45165AFD6BC0C361795C50AED25E13 where the difference is clearly observed. However what I am getting from GROMACS 5.0.5 and Origin software is something as follows https://drive.google.com/file/d/0B7SBnQ5YXQSLYUxiSk9aRVIwbzg/view?usp=sharing Is there any workaround to achieve what I am looking for? Many thanks is advance. Soumadwip Ghosh Research Fellow IITB Mumbai India -- 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 * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
