[gmx-users] binding delta G, H and S for ion-protein
Dear lloyd riggs Thanks for your consideratiuon You said " I have done this with a steered MD, using covarience " Please give me paper of your study (DOI or web page address) Best wishes -- 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] Cavity size calculation
On 2014-03-19 06:21, Praveen Kumar wrote: Dear all, I want to calculate cavity size inside some liquid in which CO2 is dissolved. Can somebody help me? Thanks. PRAVEEN KUMAR The development code for gromacs has a free volume calculation tool. See Environ. Sci. Technol. 47 pp. 7421-7429 (2013) -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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] creation coordinate file with special distance between system components
Dear all My system contains protein and ligand. I know if I do MD simulation, distance between protein and ligand will change. I want to have some coordinate files (gro file) such that in each of coordinate files, distance between protein and ligand be a special value. For example, coordination file number distance -- --- 10.05 20.1 30.15 40.2 . . . 98 4.9 99 4.95 1005 Is there a tool in gromacs which do this issue? I do not like use pull code. Any help will highly appreciated. -- 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] creation coordinate file with special distance between system components
Use editconf before solvating On Mar 19, 2014 9:09 AM, "Atila Petrosian" wrote: > Dear all > > My system contains protein and ligand. I know if I do MD simulation, > distance between protein and ligand will change. I want to have some > coordinate files (gro file) such that in each of coordinate files, distance > between protein and ligand be a special value. > > For example, > > coordination file number distance > -- --- > 10.05 > 20.1 > 30.15 > 40.2 > . > . > . > 98 4.9 > 99 4.95 > 1005 > > > Is there a tool in gromacs which do this issue? > > I do not like use pull code. > > Any help will highly appreciated. > -- > 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.
[gmx-users] constraint pulling
Dear Justin My system contains lipid + drug + water molecules. At first, I put drug molecule in middle of bilayer. Based on your tutorial, after minimization and equilibration, I generated configurations. After using distance.pl script, summary_distances.dat file is irregular such that no increasing trend is not seen in the distances. Some times distance increased and some time decreased. Is there problem in generating configuration step? pull code part of mdp file is as follows: pull = constraint pull_geometry = distance pull_constr_tol = 1e-6 pull_dim = N N Y pull_ngroups= 1 pull_group0 = CHOL_DOPC pull_group1 = drug pull_vec1 = 0 0 1 pull_rate1= 0 pull-start = yes How to resolve this issue? Best wishes -- 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] Is cholesterol model available in Charmm36 ff?
Thanks very much again for the updated charmm36 ff for Gromacs (http://mackerell.umaryland.edu/CHARMM_ff_params.html). Comparison of CHL1 residue records reveals only atom ordering difference for the atoms from 2 to 4 inclusive. In your version these atoms are ordered as follows: Probably this order is somewhat outdated since in the December release of the charmm36 the order has been changed to make the hydrogen atoms follow the heavy atoms i.e.: This kind of atom ordering difference is probably not a problem for Gromacs, but probably to be compatible with charmm36 one may consider reordering of these atoms? Thanks a lot in advance for any comment. -- View this message in context: http://gromacs.5086.x6.nabble.com/Is-cholesterol-model-available-in-Charmm36-ff-tp5014664p5015259.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] constraint pulling
Am 17.03.2014 20:11, schrieb gromacs.org_gmx-users-requ...@maillist.sys.kth.se: Dear gromacs users > >I will use pull = constraint (constraint pulling) for PMF calculations. > >There is a tutorial about PMF from Justin in which he used >pull = umbrella (umbrella sampling). > >In justin tutorial, step are as follows: > >1) preparation of system > >2) minimization & equilibration > >3) generate configuration > >4) umbrella sampling > >5) WHAM which gives PMF curve > > >I conceive in my case (pull = constraint), steps 1, 2 and 3 are similar to > >justin case (pull = umbrella). Since, WHAM analyzes output files > >generated by umbrella sampling, I have not idea about steps 4 and 5. > >I did not know how to obtain PMF curve in my case. > >If my notion is wrong, please give me more explanation such that I do > >this PMF calculation using constraint pulling method. Please tell me steps >needed for > >constraint pulling. > >Is there a tutorial about PMF calculation using constraint pulling method? > If you're using a constraint to preserve distances along the reaction coordinate, there's nothing to de-bias. There is no force constant for constraint pulling, so you can't run WHAM on its output. The constraint method fixes the distance, whereas the umbrella method is a harmonic bias (which is what you need for umbrella sampling, hence the name). If you did the "umbrella sampling" with the constraint method, there's nothing you're going to get out of it. -Justin The basic simulations are in both cases similar (as is the idea), but point (4) and (5) differ somewhat. For the constraint simulations: 4) Where umbrella sampling restraints the distances, one constrains here the distances. That's all... One thing to note (which goes also to point 3): In umbrella sampling the system can move somewhat along the reaction coordinate, with the constraints not -> This mean with the constraint pulling one should use a smaller spacing then for umbrella sampling. 5) De-bias / Calculate the PMF For the constraint pulling it's just integrating the constraint force along your reaction coordinate (in principle) - no WHAM as Justin said: -> V_pmf = - \int (R -> R_max) F_c(r) dr Tricky part is your reaction coordinate. The above holds only true if you have a linear reaction coordinate and the force acts only in one direction. For more complicate reaction coordinates it becomes more complicate. For a linear reaction coordinate where the force acts along all three axis it's: V_pmf = - \int (R -> R_max) [F_c(r) + 2 k_B T / r ] dr to 3) Easiest way to get evenly spaced configuration is using the pull code with constraints. If one uses a harmonic (/ umbrella) potential, one has fluctuations, which might are annoying in that case. Greetings Thomas -- 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] Is cholesterol model available in Charmm36 ff?
On 3/19/14, 5:06 AM, davhak wrote: Thanks very much again for the updated charmm36 ff for Gromacs (http://mackerell.umaryland.edu/CHARMM_ff_params.html). Comparison of CHL1 residue records reveals only atom ordering difference for the atoms from 2 to 4 inclusive. In your version these atoms are ordered as follows: Probably this order is somewhat outdated since in the December release of the charmm36 the order has been changed to make the hydrogen atoms follow the heavy atoms i.e.: I don't see anything printed above. This kind of atom ordering difference is probably not a problem for Gromacs, but probably to be compatible with charmm36 one may consider reordering of these atoms? Sorry, without context I really don't know what the problem might be. For any simulation software, the order of the atoms in the topology and the corresponding coordinate file need to match. What we just released is an .rtp entry for CHL1, such that you can produce the topology with pdb2gmx. The output coordinate file is guaranteed to match the topology. The order of atoms in the input coordinates relative to the .rtp entry is irrelevant; the output topology and coordinates will match. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] constraint pulling
On 3/19/14, 5:07 AM, leila karami wrote: Dear Justin My system contains lipid + drug + water molecules. At first, I put drug molecule in middle of bilayer. Based on your tutorial, after minimization and equilibration, I generated configurations. After using distance.pl script, summary_distances.dat file is irregular such that no increasing trend is not seen in the distances. Some times distance increased and some time decreased. Is there problem in generating configuration step? pull code part of mdp file is as follows: pull = constraint pull_geometry = distance pull_constr_tol = 1e-6 pull_dim = N N Y pull_ngroups= 1 pull_group0 = CHOL_DOPC pull_group1 = drug pull_vec1 = 0 0 1 pull_rate1= 0 pull-start = yes How to resolve this issue? If you're using these settings to generate configurations, you need a non-zero value of pull_rate1. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] Is cholesterol model available in Charmm36 ff?
It is good to know that pdb2gmx does not care about atoms order within a residue when comparing input coordinates and the .rtp file. Thank you very much for the information. -- View this message in context: http://gromacs.5086.x6.nabble.com/Is-cholesterol-model-available-in-Charmm36-ff-tp5014664p5015265.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] topology file
I create a parallel job file with the following content #$ -N prep66 #$ -pe openmpi* 12 #$ -cwd #$ -q medium* mpirun -np 12 /data/apps/gromacs/4.6.1/mpi/bin/editconf_mpi -f 66.pdb -o cnt.gro -bt cubic -box 5 5 5 -c mpirun -np 12 /data/apps/gromacs/4.6.1/mpi/bin/g_x2top_mpi -f cnt.gro -o cnt.top -ff opls -name CNT mpirun -np 12 /data/apps/gromacs/4.6.1/mpi/bin/genbox_mpi -cp cnt.gro -cs spc216.gro -p cnt.top -o cntsol.gro mpirun -np 12 /data/apps/gromacs/4.6.1/mpi/bin/genrestr_mpi -f cntsol.gro During the process of running it creates several temp.top files which have the correct output, however the final topology file I get has zero output. I would like to know if I am doing anything wrong. Regards, Michelle -- View this message in context: http://gromacs.5086.x6.nabble.com/topology-file-tp5015266.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] topology file
On 3/19/14, 2:22 PM, Michelle Aranha wrote: I create a parallel job file with the following content #$ -N prep66 #$ -pe openmpi* 12 #$ -cwd #$ -q medium* mpirun -np 12 /data/apps/gromacs/4.6.1/mpi/bin/editconf_mpi -f 66.pdb -o cnt.gro -bt cubic -box 5 5 5 -c mpirun -np 12 /data/apps/gromacs/4.6.1/mpi/bin/g_x2top_mpi -f cnt.gro -o cnt.top -ff opls -name CNT mpirun -np 12 /data/apps/gromacs/4.6.1/mpi/bin/genbox_mpi -cp cnt.gro -cs spc216.gro -p cnt.top -o cntsol.gro mpirun -np 12 /data/apps/gromacs/4.6.1/mpi/bin/genrestr_mpi -f cntsol.gro During the process of running it creates several temp.top files which have the correct output, however the final topology file I get has zero output. I would like to know if I am doing anything wrong. The only Gromacs executable that is parallelized is mdrun. Run the others in serial. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] missing residues in PDB file
Hello dear gmx-users, I want to transform a .pdb file to a .gro file using pdb2gmx. But there are some missing residues in my .pdb file. How should I add these missing residues to the .pdb file? Any suggestion is appreciated. Thank you very much! Cheers Yanan -- 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] missing residues in PDB file
You could add them with modeller or rosseta, Andrés Ortega Ing. Electrónica Universidad del Valle El 19/03/2014, a las 14:36, "Guo, Yanan" escribió: > Hello dear gmx-users, > > I want to transform a .pdb file to a .gro file using pdb2gmx. But there are > some missing residues in my .pdb file. How should I add these missing > residues to the .pdb file? Any suggestion is appreciated. Thank you very much! > > Cheers > Yanan > -- > 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] Is cholesterol model available in Charmm36 ff?
Correct. Pdb2gmx matches atom names of coordinate files to .rtp entries, and writes files whose atom ordering matches each other, because that is what grompp requires. The new ordering need not match that of any of the inputs to pdb2gmx. If the grompp atom *naming* is mismatched, grompp informs you - just a warning, I think. Mark On Mar 19, 2014 2:47 PM, "davhak" wrote: > It is good to know that pdb2gmx does not care about atoms order within a > residue when comparing input coordinates and the .rtp file. > > Thank you very much for the information. > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Is-cholesterol-model-available-in-Charmm36-ff-tp5014664p5015265.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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.
[gmx-users] editconf -box a b c
Hi gmx users, I try to build a cubic domain with rectangular cross-section (different a, b ,c). I have used -box a b c with editconf, but I found that only first number, a, matters and volume of box is equal to a^3 with any arbitrary values of b and c. Does anybody know why? Is there any way to make a cubic box with different length along different direction? Thanks, Ehsan -- View this message in context: http://gromacs.5086.x6.nabble.com/editconf-box-a-b-c-tp5015270.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] editconf -box a b c
Thanks Justin. You meant the values of b and c does not matter at all? -- View this message in context: http://gromacs.5086.x6.nabble.com/editconf-box-a-b-c-tp5015270p5015272.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] editconf -box a b c
On 3/19/14, 5:12 PM, ehs wrote: Hi gmx users, I try to build a cubic domain with rectangular cross-section (different a, b ,c). I have used -box a b c with editconf, but I found that only first number, a, matters and volume of box is equal to a^3 with any arbitrary values of b and c. Does anybody know why? Is there any way to make a cubic box with different length along different direction? By definition, all edges of a cube are the same length. What you're asking to do is not possible. What you want is a rectangular box. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] editconf -box a b c
On 3/19/14, 5:31 PM, ehs wrote: Thanks Justin. You meant the values of b and c does not matter at all? That depends. You haven't shown us your full command (hint: always do that), but my guess is you're setting -bt cubic, in which case the last two numbers are ignored because, by definition, they can't be different from the first. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] Multi-GPU calculation
Hi, Imagine I have two nodes, each mounted with 2 GPGPUs. If I want to require two nodes and suppose there are 4 PP ranks, is there a way to use 4 GPGPUs simultaneously in Gromacs 4.6? It seems -gpu_id is not 0123 or 0101, but something else. Thank you, -- View this message in context: http://gromacs.5086.x6.nabble.com/Multi-GPU-calculation-tp5015274.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Multi-GPU calculation
Hi, You need to pass mdrun a *per-node* PP-rank-to-GPU mapping, not a global one. Hence, in your case, you should pass -gpu_id 01 (which btw is the default). Similarly, if you want four PP ranks per node with two GPUs, you pass -gpu_id 0011. Cheers, -- Szilárd On Thu, Mar 20, 2014 at 12:49 AM, arrow50311 wrote: > Hi, > > Imagine I have two nodes, each mounted with 2 GPGPUs. If I want to require > two nodes and suppose there are 4 PP ranks, is there a way to use 4 GPGPUs > simultaneously in Gromacs 4.6? It seems -gpu_id is not 0123 or 0101, but > something else. > > Thank you, > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Multi-GPU-calculation-tp5015274.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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.
[gmx-users] plotting rmsf
i have determined rmsf values for different mutants of a same protein ..now i want to plot all rmsf values on same graph after normalising..can any one please suggest me how to plot it using xmgrace?? - thanks in advance :) -- View this message in context: http://gromacs.5086.x6.nabble.com/plotting-rmsf-tp5015276.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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.
