[gmx-users] Force GROMACS 5.0 to use GPU
Dear all gromacs user, Can I force GROMACS 5.0 to use both CPU and GPU? I simulate a protein using GROMACS 5.0 installed on old Macbook Pro Mid-2009 having 2,26 Core2Duo Proc and NVIDIA GeForce 9400M supporting CUDA technology. My GPU, however has computing ability of 1.1, where GROMACS 5.0 requires CUDA-capable GPU with computing ability of 2.0. I tried to use GPU by using verlet cut-off scheme. GOMACS exactly recognised my GPU. However, GROMACS said that my GPU was incompatible as it has only computing ability of 1.1. I need to use all my macbook resources optimally. Using 1 core was painfully slow as i spent 3 weeks to completely simulate a protein having 40.000 atoms. I wish i could take 4-5 days if GROMACS use 2 cores of CPU and CUDA-capable GPU. === My best regards, Nizar Medical Faculty of Brawijaya University, Indonesia -- 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] Force GROMACS 5.0 to use GPU
On 14.07.2014 10:21, Nizar wrote: Can I force GROMACS 5.0 to use both CPU and GPU? Afaik unfortunately not. I simulate a protein using GROMACS 5.0 installed on old Macbook Pro Mid-2009 having 2,26 Core2Duo Proc and NVIDIA GeForce 9400M supporting CUDA technology. My GPU, however has computing ability of 1.1, where GROMACS 5.0 requires CUDA-capable GPU with computing ability of 2.0. I tried to use GPU by using verlet cut-off scheme. GOMACS exactly recognised my GPU. However, GROMACS said that my GPU was incompatible as it has only computing ability of 1.1. I need to use all my macbook resources optimally. Using 1 core was painfully slow as i spent 3 weeks to completely simulate a protein having 40.000 atoms. I wish i could take 4-5 days if GROMACS use 2 cores of CPU and CUDA-capable GPU. Gromacs can't be expected to run reasonably fast on low-performance components. I think you could make very good use of your laptop if you use it for input-file creation, short test runs and data presentation. For long runs, I'd generally would not recommend laptops because they aren't built for this (heat generation, component lifetime). I tried to look up some cheap components but it looks like in your country modern (haswell) i5 processors and corresponding socket 1150 mainboards aren't readily available so far. If that's the case, you could try to get parts for a older socket 1155-system (e.g. ASRock B75M mainboard, i5-3570 processor, 2 x 2GB DDR3 RAM) combined with a more modern graphics card (Geforce GTX 760 2GB). Build this box, install Linux on it (small, cheap harddisk will suffice) and use it for simulations. But these are wild guesses only, I don't really know how affordable hardware is in your country - I tried to give you some idea of what possibly to do next. Regards M. Wahab -- 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] How to calculate the COM and box vectors in umbrella sampling
Thank you for the reply and clarifications. As I mentioned I want to use a protein-ligand complex as starting structure for the US simulations. My pdb file coordinates after running regular MD is like so: TITLE Protein in water REMARKTHIS IS A SIMULATION BOX CRYST1 121.660 121.660 121.660 90.00 90.00 90.00 P 1 1 MODEL1 ATOM 1 N MET 1 94.670 85.550 30.870 1.00 0.00 ATOM 2 H1 MET 1 94.420 86.450 30.490 1.00 0.00 ATOM 3 H2 MET 1 95.360 85.740 31.570 1.00 0.00 ATOM 4 H3 MET 1 95.170 85.100 30.130 1.00 0.00 ATOM 5 CA MET 1 93.480 84.830 31.330 1.00 0.00 ATOM 6 CB MET 1 93.780 83.330 31.470 1.00 0.00 ATOM 7 CG MET 1 92.600 82.360 31.420 1.00 0.00 ATOM 8 SD MET 1 91.600 82.470 32.940 1.00 0.00 ATOM 9 CE MET 1 92.600 81.570 34.100 1.00 0.00 ATOM 10 C MET 1 92.900 85.380 32.640 1.00 0.00 ATOM 11 O MET 1 93.370 84.960 33.700 1.00 0.00 . (Cont'd) ATOM 2418 1HD2 ASN 245 84.700 92.730 16.110 1.00 0.00 ATOM 2419 2HD2 ASN 245 83.050 92.490 16.650 1.00 0.00 ATOM 2420 C ASN 245 85.290 91.320 11.590 1.00 0.00 ATOM 2421 O1 ASN 245 85.350 92.260 10.770 1.00 0.00 ATOM 2422 O2 ASN 245 86.340 90.700 11.870 1.00 0.00 ATOM 2423 C1 UNL 246 63.920 76.740 32.640 1.00 0.00 ATOM 2424 C10 UNL 246 62.670 77.230 31.920 1.00 0.00 ATOM 2425 O12 UNL 246 63.010 77.210 30.530 1.00 0.00 ATOM 2426 C13 UNL 246 62.540 76.160 29.810 1.00 0.00 ATOM 2427 O3 UNL 246 61.390 76.200 29.360 1.00 0.00 ATOM 2428 C5 UNL 246 63.570 75.060 29.560 1.00 0.00 ATOM 2429 C6 UNL 246 63.090 73.730 28.980 1.00 0.00 ATOM 2430 C14 UNL 246 64.140 72.840 28.820 1.00 0.00 ATOM 2431 C9 UNL 246 64.070 71.590 29.410 1.00 0.00 ATOM 2432 H9 UNL 246 63.240 71.350 30.080 1.00 0.00 ATOM 2433 C7 UNL 246 65.070 73.160 27.840 1.00 0.00 ATOM 2434 H7 UNL 246 65.080 74.110 27.310 1.00 0.00 ATOM 2435 C8 UNL 246 66.030 72.210 27.500 1.00 0.00 ATOM 2436 H8 UNL 246 66.910 72.480 26.920 1.00 0.00 ATOM 2437 C15 UNL 246 65.960 70.960 28.120 1.00 0.00 ATOM 2438 O4 UNL 246 66.940 70.070 27.810 1.00 0.00 ATOM 2439 H4 UNL 246 66.830 69.200 28.290 1.00 0.00 ATOM 2440 C16 UNL 246 65.040 70.640 29.110 1.00 0.00 ATOM 2441 O11 UNL 246 65.090 69.340 29.480 1.00 0.00 ATOM 2442 C2 UNL 246 64.210 68.750 30.450 1.00 0.00 TER ENDMDL When I use the command pdb2gmx -f input.pdb -ignh -ter -o complex.gro to build the complex as the tutorial mentions, I get an error as such Fatal error: Residue 'UNL' not found in residue topology database I realize this is because the ligand itp file is not in the directory in use. Hence I separated the protein and ligand coordinates and generated a lig.gro and lig.itp file from PRODRG, and then incorporated this itp file topology into topol.top. Is this correct? I am not sure if only the protein will be restrained or both the protein and ligand will be restrained during the pulling simulations? On Thu, Jul 10, 2014 at 6:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/10/14, 1:47 AM, Maziya Ibrahim wrote: Dear all, I want to carry out umbrella sampling on a protein-ligand complex, that was already subjected to regular MD simulation for a few nanoseconds. How should I calculate the optimum pull distance and box size to be used? The length of the vector should be sufficient to at least preclude short-range nonbonded interactions and any water-mediated effects between the protein and ligand. It's not possible to achieve total non-interaction in a periodic cell with PME. Is there a default value that can be applied? No. Also how to calculate the center of mass of the protein and the box vectors? g_traj -ox -com with suitable index groups will tell you the COM positions of anything, though simply using the protein as the reference group may not be appropriate, depending on the geometry of the system. The box vectors are in the coordinate file, either the final line of a .gro file or the CRYST1 line of a .pdb file. -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
[gmx-users] (no subject)
Dear colleagues, Firstly, I want to thank Justin Lemkul for helping me on the topic polarizable water and non-polarizable alkanes. Now I have to simulate systems that consist of polarizable water and polarizable alkanes. The chosen force field is CHARMM with Drude oscillators. I am trying to use the python script cgenff_charmm2gmx.py to generate the needed files, but the following error occurs: NOTE1: Code tested with python 2.7.3. Your version: 2.6.6 (r266:84292, Jan 22 2014, 09:42:36) [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)] NOTE2: Please be sure to use the same version of CGenFF in your simulations that was used during parameter generation: --Version of CGenFF detected in charmm36-mar2014.ff//forcefield.doc : 2b8 NOTE3: In order to avoid duplicated parameters, do NOT select the 'Include parameters that are already in CGenFF' option when uploading a molecule into CGenFF. error in atomgroup.py: read_mol2_coor_only: natoms in mol2 .ne. top 17 0 I found that another person had this problem, but I still could not fix it. I have attached the files I am using. The command line I enter is: ./cgenff_charmm2gmx.py PENT pentane.mol2 ./drude_toppar_oct13/toppar_drude_model_2013a.str charmm36-mar2014.ff I will really appreciate if someone could help me, Thanks in advance, Yana -- 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] pdb2gmx
Thank you very much, I have one question for you. I would like to extract some information about salt bridge interactions (without using the gromacs command g_saltbr because it gave me some problems) between some atoms (charged negatively) of a type of monomer and some atoms (charged positively )of another type of monomer. So I created the two lists of atoms with g_select, and I made a file index like that: [ N_CRL ] 300 321 342 363 384 405 426 447 468 489 510 531 552 573 594 615 636 657 678 699 720 741 762 783 804 825 846 867 888 909 930 951 972 993 1014 1035 1056 1077 1098 1119 [ OX_ITA ] 168 181 194 207 220 233 246 259 272 285 and then I used g_hbond to extract the contacts of these 2 lists of atoms within 4 Å. in this way: g_hbond_d -f eq4.gro -s eq3.tpr -n index.ndx -hbn hbond.ndx -contact -r2 0.4 -r 0.4 I noticed a strange thing, if I change the order of the groups in the index.ndx file,like that: [ OX_ITA ] 168 181 194 207 220 233 246 259 272 285 [ N_CRL ] 300 321 342 363 384 405 426 447 468 489 510 531 552 573 594 615 636 657 678 699 720 741 762 783 804 825 846 867 888 909 930 951 972 993 1014 1035 1056 1077 1098 1119 I obtain no contacts, and it is wrong because actually I didn't change the atoms of the groups. Could you help me about it ? Thank you very much Mirko On Wednesday, June 25, 2014 12:00 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/25/14, 4:44 AM, mirko busato wrote: Thank you very much, In my analysis ,I would like to consider Hydrogen bonds involving S atom as well. I think that g_hbond is not built to manage Hydrogen bonds with S. Do you know if there are available scripts? or Could you suggest me something to solve this problem? g_hbond is hard-coded to deal with certain groups, so it's not very flexible. The workaround we've used in the past is to simply rename the S atoms of interest as O in the .top file, generate a .tpr with those dummy names, and run g_hbond using that .tpr file. -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] Problem related to solvating CNT and then removing out the molecules inside CNT
On 7/14/14, 12:28 AM, vivek sinha wrote: Hey Justin, I am really having a hard time using GROMACS for my simulation. When trying to equilibrate in NVT ensemble I am getting this warning. --- WARNING: Listed nonbonded interaction between particles 227 and 230 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. -- Can you please look over my nvt.mdp file -- title= CNT in water define= -DPOSRES; position restrain the protein ; Run parameters integrator= md; leap-frog integrator nsteps= 5; 2 * 5 = 100 ps dt= 0.002; 2 fs ; Output control nstxout= 500; save coordinates every 1.0 ps nstvout= 500; save velocities every 1.0 ps nstenergy= 500; save energies every 1.0 ps nstlog= 500; update log file every 1.0 ps ; Bond parameters continuation= no; first dynamics run constraint_algorithm= lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching cutoff-scheme = Verlet ns_type= grid; search neighboring grid cells nstlist= 10; 20 fs, largely irrelevant with Verlet rcoulomb= 0.9; short-range electrostatic cutoff (in nm) rvdw= 0.9; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.12; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= non-water SOL; two coupling groups - more accurate tau_t= 0.1 0.1 ; time constant, in ps ref_t= 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl= no ; no pressure coupling in NVT ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= yes; assign velocities from Maxwell distribution gen_temp= 300; temperature for Maxwell distribution gen_seed= -1; generate a random seed -- Please suggest how can I correct the problem. If the CNT is infinite along some axis, you need to use the periodic_molecules keyword, otherwise bonded interactions are assigned totally within the unit cell and you get nonsensical geometry. As to your other question, cutoffs of 1.0 are commonly used with OPLS. -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] How to calculate the COM and box vectors in umbrella sampling
On 7/14/14, 5:48 AM, Maziya Ibrahim wrote: Thank you for the reply and clarifications. As I mentioned I want to use a protein-ligand complex as starting structure for the US simulations. My pdb file coordinates after running regular MD is like so: TITLE Protein in water REMARKTHIS IS A SIMULATION BOX CRYST1 121.660 121.660 121.660 90.00 90.00 90.00 P 1 1 MODEL1 ATOM 1 N MET 1 94.670 85.550 30.870 1.00 0.00 ATOM 2 H1 MET 1 94.420 86.450 30.490 1.00 0.00 ATOM 3 H2 MET 1 95.360 85.740 31.570 1.00 0.00 ATOM 4 H3 MET 1 95.170 85.100 30.130 1.00 0.00 ATOM 5 CA MET 1 93.480 84.830 31.330 1.00 0.00 ATOM 6 CB MET 1 93.780 83.330 31.470 1.00 0.00 ATOM 7 CG MET 1 92.600 82.360 31.420 1.00 0.00 ATOM 8 SD MET 1 91.600 82.470 32.940 1.00 0.00 ATOM 9 CE MET 1 92.600 81.570 34.100 1.00 0.00 ATOM 10 C MET 1 92.900 85.380 32.640 1.00 0.00 ATOM 11 O MET 1 93.370 84.960 33.700 1.00 0.00 . (Cont'd) ATOM 2418 1HD2 ASN 245 84.700 92.730 16.110 1.00 0.00 ATOM 2419 2HD2 ASN 245 83.050 92.490 16.650 1.00 0.00 ATOM 2420 C ASN 245 85.290 91.320 11.590 1.00 0.00 ATOM 2421 O1 ASN 245 85.350 92.260 10.770 1.00 0.00 ATOM 2422 O2 ASN 245 86.340 90.700 11.870 1.00 0.00 ATOM 2423 C1 UNL 246 63.920 76.740 32.640 1.00 0.00 ATOM 2424 C10 UNL 246 62.670 77.230 31.920 1.00 0.00 ATOM 2425 O12 UNL 246 63.010 77.210 30.530 1.00 0.00 ATOM 2426 C13 UNL 246 62.540 76.160 29.810 1.00 0.00 ATOM 2427 O3 UNL 246 61.390 76.200 29.360 1.00 0.00 ATOM 2428 C5 UNL 246 63.570 75.060 29.560 1.00 0.00 ATOM 2429 C6 UNL 246 63.090 73.730 28.980 1.00 0.00 ATOM 2430 C14 UNL 246 64.140 72.840 28.820 1.00 0.00 ATOM 2431 C9 UNL 246 64.070 71.590 29.410 1.00 0.00 ATOM 2432 H9 UNL 246 63.240 71.350 30.080 1.00 0.00 ATOM 2433 C7 UNL 246 65.070 73.160 27.840 1.00 0.00 ATOM 2434 H7 UNL 246 65.080 74.110 27.310 1.00 0.00 ATOM 2435 C8 UNL 246 66.030 72.210 27.500 1.00 0.00 ATOM 2436 H8 UNL 246 66.910 72.480 26.920 1.00 0.00 ATOM 2437 C15 UNL 246 65.960 70.960 28.120 1.00 0.00 ATOM 2438 O4 UNL 246 66.940 70.070 27.810 1.00 0.00 ATOM 2439 H4 UNL 246 66.830 69.200 28.290 1.00 0.00 ATOM 2440 C16 UNL 246 65.040 70.640 29.110 1.00 0.00 ATOM 2441 O11 UNL 246 65.090 69.340 29.480 1.00 0.00 ATOM 2442 C2 UNL 246 64.210 68.750 30.450 1.00 0.00 TER ENDMDL When I use the command pdb2gmx -f input.pdb -ignh -ter -o complex.gro to build the complex as the tutorial mentions, I get an error as such Fatal error: Residue 'UNL' not found in residue topology database I realize this is because the ligand itp file is not in the directory in use. Hence I separated the protein and ligand coordinates and generated a lig.gro and lig.itp file from PRODRG, and then incorporated this itp file topology into topol.top. Is this correct? I am not sure if only the Make sure you correct the PRODRG topology; its charges and charge groups are going to be unreliable. protein will be restrained or both the protein and ligand will be restrained during the pulling simulations? The restraint potential is applied to whatever groups you assign. Without seeing exactly what you're doing (i.e. post an .mdp file for us), there's no way to answer this. -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] (no subject)
On 7/14/14, 6:17 AM, Yana Tsoneva wrote: Dear colleagues, Firstly, I want to thank Justin Lemkul for helping me on the topic polarizable water and non-polarizable alkanes. Now I have to simulate systems that consist of polarizable water and polarizable alkanes. The chosen force field is CHARMM with Drude oscillators. I am trying to use the python script cgenff_charmm2gmx.py to generate the needed files, but the following error occurs: NOTE1: Code tested with python 2.7.3. Your version: 2.6.6 (r266:84292, Jan 22 2014, 09:42:36) [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)] NOTE2: Please be sure to use the same version of CGenFF in your simulations that was used during parameter generation: --Version of CGenFF detected in charmm36-mar2014.ff//forcefield.doc : 2b8 NOTE3: In order to avoid duplicated parameters, do NOT select the 'Include parameters that are already in CGenFF' option when uploading a molecule into CGenFF. error in atomgroup.py: read_mol2_coor_only: natoms in mol2 .ne. top 17 0 I found that another person had this problem, but I still could not fix it. I have attached the files I am using. The command line I enter is: ./cgenff_charmm2gmx.py PENT pentane.mol2 ./drude_toppar_oct13/toppar_drude_model_2013a.str charmm36-mar2014.ff I will really appreciate if someone could help me, The CGenFF conversion script is intended to process a .mol2 file with a single molecule and a corresponding .str file with a single molecule. What you're trying to do is doomed to fail for two reasons: 1. The toppar_drude_model_2013a.str file contains all model compounds we used in the parametrization of the Drude FF 2. CHARMM36 from March 2014 is an additive force field. Please also note that our parametrization of the Drude FF is with thermalized, mass-bearing Drude particles. In principle, these types of systems can be simulated in Gromacs using an SCF procedure to solve the positions of the Drude particles, but not out of the box in the case of mass-bearing Drudes. I am working on implementing all of the necessary algorithms to make this a reality, but the code is not yet suitable for public consumption. Using massless Drudes/shells will work fine, but strictly speaking that is not the Drude FF that we have parametrized. -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] g_hbond
On 7/14/14, 7:44 AM, mirko busato wrote: Dear Users, I have one question for you. I would like to extract some information about salt bridge interactions (without using the gromacs command g_saltbr because it gave me some problems) between some atoms (charged negatively) of a type of monomer and some atoms (charged positively )of another type of monomer. So I created the two lists of atoms with g_select, and I made a file index like that: [ N_CRL ] 300 321 342 363 384 405 426 447 468 489 510 531 552 573 594 615 636 657 678 699 720 741 762 783 804 825 846 867 888 909 930 951 972 993 1014 1035 1056 1077 1098 1119 [ OX_ITA ] 168 181 194 207 220 233 246 259 272 285 and then I used g_hbond to extract the contacts of these 2 lists of atoms within 4 Å. in this way: g_hbond_d -f eq4.gro -s eq3.tpr -n index.ndx -hbn hbond.ndx -contact -r2 0.4 -r 0.4 I wouldn't use g_hbond like this; g_mindist -on is more straightforward for calculating simple contacts. I noticed a strange thing, if I change the order of the groups in the index.ndx file,like that: [ OX_ITA ] 168 181 194 207 220 233 246 259 272 285 [ N_CRL ] 300 321 342 363 384 405 426 447 468 489 510 531 552 573 594 615 636 657 678 699 720 741 762 783 804 825 846 867 888 909 930 951 972 993 1014 1035 1056 1077 1098 1119 I obtain no contacts, and it is wrong because actually I didn't change the atoms of the groups. Could you help me about it ? Order of the groups in the index file is irrelevant; it doesn't seem likely that this is the only issue. -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] g_hbond
On 7/14/14, 7:44 AM, mirko busato wrote: Dear Users, I have one question for you. I would like to extract some information about salt bridge interactions (without using the gromacs command g_saltbr because it gave me some problems) between some atoms (charged negatively) of a type of monomer and some atoms (charged positively )of another type of monomer. So I created the two lists of atoms with g_select, and I made a file index like that: [ N_CRL ] 300 321 342 363 384 405 426 447 468 489 510 531 552 573 594 615 636 657 678 699 720 741 762 783 804 825 846 867 888 909 930 951 972 993 1014 1035 1056 1077 1098 1119 [ OX_ITA ] 168 181 194 207 220 233 246 259 272 285 and then I used g_hbond to extract the contacts of these 2 lists of atoms within 4 Å. in this way: g_hbond_d -f eq4.gro -s eq3.tpr -n index.ndx -hbn hbond.ndx -contact -r2 0.4 -r 0.4 I wouldn't use g_hbond like this; g_mindist -on is more straightforward for calculating simple contacts. I noticed a strange thing, if I change the order of the groups in the index.ndx file,like that: [ OX_ITA ] 168 181 194 207 220 233 246 259 272 285 [ N_CRL ] 300 321 342 363 384 405 426 447 468 489 510 531 552 573 594 615 636 657 678 699 720 741 762 783 804 825 846 867 888 909 930 951 972 993 1014 1035 1056 1077 1098 1119 I obtain no contacts, and it is wrong because actually I didn't change the atoms of the groups. Could you help me about it ? Order of the groups in the index file is irrelevant; it doesn't seem likely that this is the only issue. -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] g_hbond
thank you very much, I read the manual of g_mindist but seem produce in output only the number of contacts and the minimum distance . For my problem I would like to know all the atoms involved (all the contacts) within of 4 Å. so I can understand which atoms can do salt bridge interactions. Do you know a way to do this with g_mindist command? Thank you very much, Mirko On Monday, July 14, 2014 2:02 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/14/14, 7:44 AM, mirko busato wrote: Dear Users, I have one question for you. I would like to extract some information about salt bridge interactions (without using the gromacs command g_saltbr because it gave me some problems) between some atoms (charged negatively) of a type of monomer and some atoms (charged positively )of another type of monomer. So I created the two lists of atoms with g_select, and I made a file index like that: [ N_CRL ] 300 321 342 363 384 405 426 447 468 489 510 531 552 573 594 615 636 657 678 699 720 741 762 783 804 825 846 867 888 909 930 951 972 993 1014 1035 1056 1077 1098 1119 [ OX_ITA ] 168 181 194 207 220 233 246 259 272 285 and then I used g_hbond to extract the contacts of these 2 lists of atoms within 4 Å. in this way: g_hbond_d -f eq4.gro -s eq3.tpr -n index.ndx -hbn hbond.ndx -contact -r2 0.4 -r 0.4 I wouldn't use g_hbond like this; g_mindist -on is more straightforward for calculating simple contacts. I noticed a strange thing, if I change the order of the groups in the index.ndx file,like that: [ OX_ITA ] 168 181 194 207 220 233 246 259 272 285 [ N_CRL ] 300 321 342 363 384 405 426 447 468 489 510 531 552 573 594 615 636 657 678 699 720 741 762 783 804 825 846 867 888 909 930 951 972 993 1014 1035 1056 1077 1098 1119 I obtain no contacts, and it is wrong because actually I didn't change the atoms of the groups. Could you help me about it ? Order of the groups in the index file is irrelevant; it doesn't seem likely that this is the only issue. -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] Problem with g_chi options
Hi! Thanks for your reply Justin! I have tried using a tpr file instead of a gro file, but that makes no difference. I still have the same problem! Does anybody have another idea? Thanks in advance! Anna On 07/09/2014 07:24 PM, Justin Lemkul wrote: On 7/9/14, 5:51 AM, Anna Stopka wrote: Hi everybody, I wrote last week, but nobody answered. So I write again, still having the same problem: I want do an analysis of my simulation with the tool g_chi. The problem is, that the optional output options don't work. I use the following command: g_chi -s config.gro -f traj.xtc -oh -all and all I get are the standard output files chi.log and order.xvg. I am not sure if it has something to do with the following warning I get: WARNING: not all dihedrals found in topology (only 1056 out of 1746)! Honestly, I don't understand why I get this warning, because all the input files are fine. Have you tried using a .tpr file instead of a .gro file as the structure passed to -s? I don't know how there can be any interpretation of a topology, given the fact that you haven't passed any topological information to g_chi. -Justin -- 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] Problem related to solvating CNT and then removing out the molecules inside CNT
Hi Justin, I dont have the periodic molecules so do I include anything in the .mdp file? Also when I grompp this I get no warning or error or note. But when I mdrun it, I get WARNING: Listed nonbonded interaction between particles 35 and 114 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. and then the program terminates after displaying a segmentation fault error. Please provide any valuable suggestions. Thanks, Vivek Sinha On Mon, Jul 14, 2014 at 8:52 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/14/14, 12:28 AM, vivek sinha wrote: Hey Justin, I am really having a hard time using GROMACS for my simulation. When trying to equilibrate in NVT ensemble I am getting this warning. --- WARNING: Listed nonbonded interaction between particles 227 and 230 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. -- Can you please look over my nvt.mdp file -- title= CNT in water define= -DPOSRES; position restrain the protein ; Run parameters integrator= md; leap-frog integrator nsteps= 5; 2 * 5 = 100 ps dt= 0.002; 2 fs ; Output control nstxout= 500; save coordinates every 1.0 ps nstvout= 500; save velocities every 1.0 ps nstenergy= 500; save energies every 1.0 ps nstlog= 500; update log file every 1.0 ps ; Bond parameters continuation= no; first dynamics run constraint_algorithm= lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching cutoff-scheme = Verlet ns_type= grid; search neighboring grid cells nstlist= 10; 20 fs, largely irrelevant with Verlet rcoulomb= 0.9; short-range electrostatic cutoff (in nm) rvdw= 0.9; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.12; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= non-water SOL; two coupling groups - more accurate tau_t= 0.1 0.1 ; time constant, in ps ref_t= 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl= no ; no pressure coupling in NVT ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= yes; assign velocities from Maxwell distribution gen_temp= 300; temperature for Maxwell distribution gen_seed= -1; generate a random seed -- Please suggest how can I correct the problem. If the CNT is infinite along some axis, you need to use the periodic_molecules keyword, otherwise bonded interactions are assigned totally within the unit cell and you get nonsensical geometry. As to your other question, cutoffs of 1.0 are commonly used with OPLS. -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
Re: [gmx-users] Having Problem with Gromacs Regressiontests
Hi, Results: All 16 simple tests PASSED All 19 complex tests PASSED All 142 kernel tests PASSED All 9 freeenergy tests PASSED All 12 rotation tests PASSED All 0 extra tests PASSED All 42 pdb2gmx tests PASSED Thank you very much On Sun, Jul 13, 2014 at 6:00 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/13/14, 4:02 PM, Todor Antonijevic wrote: Hi, I am unable to test my new Gromacs 4.6.6 installation. Here are the steps that I perform (following http://www.gromacs.org/Developer_Zone/Programming_Guide/Regression_Tests) : @ubuntu:~$ git clone https://gerrit.gromacs.org/regressiontests Cloning into 'regressiontests'... remote: Counting objects: 3466, done remote: Finding sources: 100% (352/352) remote: Total 11744 (delta 194), reused 11695 (delta 194) Receiving objects: 100% (11744/11744), 168.70 MiB | 213 KiB/s, done. Resolving deltas: 100% (8689/8689), done. @ubuntu:~$ cd /home//regressiontests/ @ubuntu:~/regressiontests$ ./gmxtest.pl all -noverbose *ERROR: Can not find executable gmx pdb2gmx in your path.* *Please source GMXRC and try again.* @ubuntu:~/regressiontests$ which GMXRC /usr/local/gromacs/bin/GMXRC @ubuntu:~/regressiontests$ *source /usr/local/gromacs/bin/GMXRC* @ubuntu:~/regressiontests$ ./gmxtest.pl all -noverbose *ERROR: Can not find executable gmx pdb2gmx in your path.* *Please source GMXRC and try again.* I would appreciate if you could help me on this matter. When you checkout the code or tests from git, you're automatically on the master branch, which uses 5.0 syntax and command names. If you want to test another version, you have to switch to that branch. For 4.6.6, do: cd regressiontests git checkout release-4-6 Then run the tests. -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. -- 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] perl script running
Dear users how can i running perl script files in my linux ? is this correct? chmod +x *.pl perl ./ *.pl *.xpm thanks for your reply -- 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] perl script running
On 14.07.2014 21:05, elham tazikeh wrote: how can i running perl script files in my linux ? This is not a Gromacs-related question. Questions like these are best answered in appropriate sites like stackoverflow.com is this correct? chmod +x *.pl yes, but most probably unnecessary perl ./ *.pl *.xpm The first argument (the current directory) is no valid command line parameter for the perl interpreter at this point. For th other two parameters, the Linux-shell will expand the '*' (wildcard) to all matching names from the current directory in any order the shell finds reasonable. This is probably not what you want. Ask your question on: http://stackoverflow.com or (maybe better) on: http://unix.stackexchange.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] Problem related to solvating CNT and then removing out the molecules inside CNT
On 7/14/14, 9:38 AM, vivek sinha wrote: Hi Justin, I dont have the periodic molecules so do I include anything in the .mdp file? Also when I grompp this I get no warning or error or note. But when I mdrun it, I get WARNING: Listed nonbonded interaction between particles 35 and 114 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. and then the program terminates after displaying a segmentation fault error. Please provide any valuable suggestions. Your system is blowing up. It's a hard situation to diagnose with limited information, but something is almost certainly wrong with your topology. http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System -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] g_energy help
Thank you Justin ,for the help , but i really dont get it, energy tyoe CNT-CNT mean within ? , you mean inside? or al the energy that the CNT is experiment by the nonbonds of itself? thank you -- 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.
