Re: [gmx-users] (no subject)
On 2/28/14, 5:38 AM, abhijit Kayal wrote: Dear Gromacs users, My system contained CNT+ water. I have created a dynamically index.ndx file which contain the number of water molecules in each frame inside cnt. Now I want to study the dipole orientation of these water molecules. But I can't select all the groups at a time. From the mailing lists search I came to know that any gromacs analysis tools can't do this. So is there any other way to do these type of analysis. I am using gromacs 4.5.5. You have to analyze each frame individually rather than processing the trajectory in one pass. With a simple shell script, you can loop through the index groups, write out a corresponding frame from the trajectory, then analyze it. -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)
Thanks Justin for the help. But if I want to look the dipole auto correlation or hydrogen bond dynamics ... is that possible? On Fri, Feb 28, 2014 at 4:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/28/14, 5:38 AM, abhijit Kayal wrote: Dear Gromacs users, My system contained CNT+ water. I have created a dynamically index.ndx file which contain the number of water molecules in each frame inside cnt. Now I want to study the dipole orientation of these water molecules. But I can't select all the groups at a time. From the mailing lists search I came to know that any gromacs analysis tools can't do this. So is there any other way to do these type of analysis. I am using gromacs 4.5.5. You have to analyze each frame individually rather than processing the trajectory in one pass. With a simple shell script, you can loop through the index groups, write out a corresponding frame from the trajectory, then analyze it. -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. -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- 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 2/28/14, 6:36 AM, abhijit Kayal wrote: Thanks Justin for the help. But if I want to look the dipole auto correlation or hydrogen bond dynamics ... is that possible? Each frame is just a time point in the trajectory. Concatenate the individual output and you get a time series. -Justin On Fri, Feb 28, 2014 at 4:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/28/14, 5:38 AM, abhijit Kayal wrote: Dear Gromacs users, My system contained CNT+ water. I have created a dynamically index.ndx file which contain the number of water molecules in each frame inside cnt. Now I want to study the dipole orientation of these water molecules. But I can't select all the groups at a time. From the mailing lists search I came to know that any gromacs analysis tools can't do this. So is there any other way to do these type of analysis. I am using gromacs 4.5.5. You have to analyze each frame individually rather than processing the trajectory in one pass. With a simple shell script, you can loop through the index groups, write out a corresponding frame from the trajectory, then analyze it. -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. -- == 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] Can i use GPU for my desktop computer
Dear GMX users, I learned that GPU can acceleprate the speed of MD, but i do not know whether it is possible to use GPU on desktop. Our Lab does not have supercomputer, and i can only run gromacs by using normal comuters. The computer i am using is hp，and it has 8 i7 cores. Whan kind of GPU shall i use if it is possible to run GPU acceleration on desktop computer ? Best regards Fugui -- 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] ref_t and gen_temp
Hi all, I want to run some simulations at different temperatures (protein and solvent) changing the ref_t values. First at 300K, then 320K so on.. So, my question is: should I also change the gen_temp value while changing the ref_t value? Thanks and regards, Turgay -- 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] ref_t and gen_temp
On 2/28/14, 10:21 AM, Turgay Cakmak wrote: Hi all, I want to run some simulations at different temperatures (protein and solvent) changing the ref_t values. First at 300K, then 320K so on.. So, my question is: should I also change the gen_temp value while changing the ref_t value? Yes. -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] xpm2ps
Hello, I would like to change the scale of x axis and y axis of my dssp.eps file by different amounts. Example with xpm2ps -skip command I can write out every nr-th row and nr-th column but I want every nr-th row and mr-th column. Please suggest if it is possible to do so. Thanks in advance. Nidhi -- 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] PME
Dear GMX users I run gromacs 4.6.3 in parallel for my system. My simulation box is triclinic. My MD simulation is computed on in-house Linux 64-bit Intel Core-i7. As far as I know, for triclinic box, the optimal setup will have a PME load of 0.25, so I change pme order and grid spacing in my mdp file to get this value. According to manual, I should change pme order to 6/8/10 when running in parallel. when I change it to 6, PME load become 0.33 ( 0.25). I do not know if it is correct. Please help me about this issue. Best Regards -- 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] xpm2ps
On 2014-02-28 16:39, Nidhi Katyal wrote: Hello, I would like to change the scale of x axis and y axis of my dssp.eps file by different amounts. Example with xpm2ps -skip command I can write out every nr-th row and nr-th column but I want every nr-th row and mr-th column. Please suggest if it is possible to do so. Thanks in advance. Nidhi Sure. You have to provide a .m2p file. -- 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] A question about blowing up
Hello, I am following justin lemkul's tutorials for the cyclohexane-water biphasic system using Gromos96 forcefield. Things went well till NVT equilibration where I had this Blowing up issue. Shortening the time step alone did not help, and it was difficult for me to figure out what was happening from watching the trajectory. g_energy data indicated a spike on the, short range LJ contribution at around 10ps. Then I switched off the constraints (but not for water, SETTLE still used) and ran the simulation again with a small time step. Things worked well this time , the system reaching the target temperature. I want to make sure that switching off the constraints is a reasonable thing to solve Blowing up and that it would not affect in any way the accuracy of further simulations. http://www.gromacs.org/Documentation/Terminology/Blowing_Up says that constraints are exactly not the source of the Blowing up problem. However, http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation suggests removing constraints as a solution. So, in general, is the problem solved by removing constrains, or am I cheating? Please comment. Here is the .mdp file which solved the Blowing up issue. ; 7.3.3 Run Control integrator = md tinit = 0 dt = 0.0002 nsteps = 250 comm_mode = Linear nstcomm = 1 comm_grps = CHX SOL ; 7.3.8 Output Control nstxout = 25000 nstvout = 25000 nstfout = 25000 nstlog = 100 nstenergy = 100 nstxtcout = 100 xtc_precision = 1000 xtc_grps = System energygrps = System ; 7.3.9 Neighbor Searching nstlist= 1 ns_type = grid pbc = xyz rlist = 0.9 ; 7.3.10 Electrostatics coulombtype = PME rcoulomb = 0.9 ; 7.3.11 VdW vdwtype = cut-off rvdw = 1.4 DispCorr = EnerPres ; 7.3.13 Ewald fourierspacing = 0.12 pme_order = 4 ewald_rtol= 1e-5 ; 7.3.14 Temperature Coupling tcoupl = berendsen tc_grps = CHXSOL tau_t = 0.10.1 ref_t = 298298 ; 7.3.17 Velocity Generation gen_vel = yes gen_temp= 298 gen_seed = -1 ; 7.3.18 Bonds constraints = none constraint_algorithm= LINCS continuation= no lincs_order = 4 lincs_iter = 1 lincs_warnangle = 30 ~ Thanks, Sujith. -- 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.
