Re: [gmx-users] cannot open traj.xtc
Thankyou sir, After using g_order -s md_0_1.tpr -f md_0_1.tpr.trr -n sn1.ndx -d z -od deuter_sn1.xvg the file order.xvg is created but still my file does not give any information about the system whether it is in gel phase or liquid phase. Please suggest me where i am going wrong. Thanks in advance. Regards Surbhi On Wed, Nov 18, 2015 at 6:11 PM, Justin Lemkul wrote: > > > On 11/18/15 2:45 AM, surbhi mahajan wrote: > >> Dear users, >> I am M.Sc student , I have been doing my simulations on lipids , I am >> stuck >> at the analysis part in which i want to calculate deuterium order >> parameter >> after I give the command: >> g_order -s md_0_1.tpr -n sn1.ndx -d z -od deuter_sn1.xvg >> I get the error cannot open file traj.xtc. please help me in solving this >> error. >> > > You didn't specify a trajectory file name (-f argument) so g_order looks > for the default name (traj.xtc) and it doesn't exit. Specify a proper > input file name. > > -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. > -- 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] symtab get_symtab_handle error
On 11/19/15 12:05 PM, Zhaleh Ghaemi wrote: Dear all, I'm running Gromacs 5.0 on a protein-RNA system. The simulations need to be extended. I used the replacement of the tpbconv in version 5.0, namely "gmx convert-tpr" to extend the simulations with the command: mx convert-tpr -s md.tpr -f md.cpt -extend 2 -o md2.tpr the md2.tpr file was generated with no errors, however the mdrun crashed generating this error: *Fatal error:symtab get_symtab_handle 799 not found* So my questions are, why this error is happening? and what is the correct way with which the simulations can be extended (or restarted in the case of crashed simulations) with Gromacs 5.0? Do not supply a .cpt file to convert-tpr. If a correctly generated .tpr file still generates an error, trying upgrading to the latest version (5.1.1) and try again. -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] charge calculations and topology
On 11/19/15 11:01 AM, Chetan Puri wrote: Can somebody suggest what could be the best possible way for generating small molecules topology file and charge determination ( OPLS force field) as I want carry out a simulation for miscell formation between small ligands. See http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00864 and references therein. -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] Gromacs 5.1 and 5.1.1 crash in REMD
Dear Justin and Mark Thanks for your helpful suggestions. Yes, my case is just like bug 1848 Our computing staff recompiled the 5.1.1 code with the debugger an ran a backtrace on my job, concluding that there is a bug in the code. I include their conclusions in case that might help resolve the problem- condensed backtrace follows: Krzysztof [67] 0x007a10bd in add_binr (b=0x25f11c0, nr=9, r=0x0) at /home/wmason/gromacs-5.1.1/src/gromacs/gmxlib/rbin.c:94 [4-7,12-15,20-31,60-67] 94 rbuf[i] = r[i]; 0x00725758 in global_stat (fplog=0x3543750, gs=0x3639420, cr=0x3536fa0, enerd=0x36398b0, fvir=0x0, svir=0x0, mu_tot=0x7fff6a2dfe6c, inputrec=0x35424f0, ekind=0x3635990, constr=0x363b920, vcm=0x0, nsig=0, sig=0x0, top_global=0x3541860, state_local=0x363a090, bSumEkinhOld=0, flags=146) at /home/wmason/gromacs-5.1.1/src/gromacs/mdlib/stat.cpp:229 0x0073efcd in compute_globals (fplog=0x3543750, gstat=0x3639420, cr=0x3536fa0, ir=0x35424f0, fr=0x3599df0, ekind=0x3635990, state=0x363a090, state_global=0x3543270, mdatoms=0x35cc860, nrnb=0x3599a20, vcm=0x3623b40, wcycle=0x3599340, enerd=0x36398b0, force_vir=0x0, shake_vir=0x0, total_vir=0x0, pres=0x0, mu_tot=0x7fff6a2dfe6c, constr=0x363b920, gs=0x0, bInterSimGS=0, box=0x363a0b0, top_global=0x3541860, bSumEkinhOld=0x7fff6a2dff10, flags=146) at /home/wmason/gromacs-5.1.1/src/gromacs/mdlib/md_support.cpp:342 0x004c3dca in do_md (fplog=0x0, cr=0x24a7fb0, nfile=35, fnm=0x7fffa95b48a8, oenv=0x24b46e0, bVerbose=0, bCompact=1, nstglobalcomm=20, vsite=0x252d890, constr=0x25e9a80, stepout=100, ir=0x24b2430, top_global=0x24b4760, fcd=0x24ea8b0, state_global=0x24b31c0, mdatoms=0x252d980, nrnb=0x24fa9b0, wcycle=0x24fa1b0, ed=0x0, fr=0x24fad80, repl_ex_nst=500, repl_ex_nex=0, repl_ex_seed=-1, membed=0x0, cpt_period=15, max_hours=-1, imdport=, Flags=1055744, walltime_accounting=0x2584a20) at /home/wmason/gromacs-5.1.1/src/programs/mdrun/md.cpp:969 0x004d4a64 in mdrunner (hw_opt=0x7fff6a2e1d58, fplog=0x3543750, cr=0x3536fa0, nfile=35, fnm=0x7fff6a2e15f8, oenv=0x35436d0, bVerbose=0, bCompact=1, nstglobalcomm=-1, ddxyz=0x7fff6a2e11bc, dd_node_order=1, rdd=0, rconstr=0, dddlb_opt=0x1f3b10c "auto", dlb_scale=0.80012, ddcsx=0x0, ddcsy=0x0, ddcsz=0x0, nbpu_opt=0x1f3b10c "auto", nstlist_cmdline=0, nsteps_cmdline=-2, nstepout=100, resetstep=-1, nmultisim=40, repl_ex_nst=500, repl_ex_nex=0, repl_ex_seed=-1, pforce=-1, cpt_period=15, max_hours=-1, imdport=, Flags=1055744) at /home/wmason/gromacs-5.1.1/src/programs/mdrun/runner.cpp:1270 0x004cb637 in gmx_mdrun (argc=15, argv=0x3531c20) at /home/wmason/gromacs-5.1.1/src/programs/mdrun/mdrun.cpp:537 0x0050b26b in gmx::CommandLineModuleManager::runAsMainCMain (argc=15, argv=0x7fffa95b5aa8, mainFunction=0x4c8d73 ) at /home/wmason/gromacs-5.1.1/src/gromacs/commandline/cmdlinemodulemanager.cpp:588 0x004ba316 in main (argc=15, argv=0x7fff6a2e27f8) at /home/wmason/gromacs-5.1.1/src/programs/mdrun_main.cpp:43 The error is a classic segmentation fault--caused by accessing an array out of bounds. It's a bug in the Gromacs 5.1.1 code. You will need to file a bug report with gromacs, and they will need your job input to reproduce the error, and the backtrace info above, which I've summarized if you just want to read the code yourself: "add_rbin" in gromacs-5.1.1/src/gromacs/gmxlib/rbin.c:94 called from "global_stat" in gromacs-5.1.1/src/gromacs/mdlib/stat.cpp:229 called from "compute_globals" in gromacs-5.1.1/src/gromacs/mdlib/md_support.cpp:342 called from "do_md" in /gromacs-5.1.1/src/programs/mdrun/md.cpp:969 called from "mdrunner" in gromacs-5.1.1/src/programs/mdrun/runner.cpp:1270 called from "gmx_mdrun" in gromacs-5.1.1/src/programs/mdrun/mdrun.cpp:537 The code which fails is taking a "bin" of the "gmx_global_stat" type, which holds an array of doubles and the size of the array, and tries to copy in data from a "tensor" of the force virial, during a step in which energy is computed globally. I don't have any clue what this means, except for what the low-level code says (I almost always have read the source code when debugging so I could try to explain what's happening). There are multiple possible causes for this error, such as: A. The memory allocation for the "bin" fails quietly--the array is not resized (or not the right size), and then the error occurs at the next function which tries to write data there. B. The tensor is actually not the size "DIM*DIM" (3x3 if I'm reading correctly) that the function expects. Accessing the source tensor array out-of-bounds also generates this error. C. The tensor is actually a NULL pointer. This is the most likely explanation, which one can see from the line: add_binr (b=0x25f11c0, nr=9, r=0x0) ^ Either r=NULL or the debugger is not reporting the value correctly. This would mean the program is calling "do_md" from "mdrunner" with bad parameters and not checking its parameters for errors. The error actually occurs at a
[gmx-users] symtab get_symtab_handle error
Dear all, I'm running Gromacs 5.0 on a protein-RNA system. The simulations need to be extended. I used the replacement of the tpbconv in version 5.0, namely "gmx convert-tpr" to extend the simulations with the command: mx convert-tpr -s md.tpr -f md.cpt -extend 2 -o md2.tpr the md2.tpr file was generated with no errors, however the mdrun crashed generating this error: *Fatal error:symtab get_symtab_handle 799 not found* So my questions are, why this error is happening? and what is the correct way with which the simulations can be extended (or restarted in the case of crashed simulations) with Gromacs 5.0? Thanks, Zhaleh -- 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] charge calculations and topology
Can somebody suggest what could be the best possible way for generating small molecules topology file and charge determination ( OPLS force field) as I want carry out a simulation for miscell formation between small ligands. -- 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] POPC simulation with heavy hydrogens and 4 fs timestep
On 11/19/15 7:49 AM, Ganesh Shahane wrote: Dear Gromacs Users, I have been trying to simulate a pure POPC bilayer with a timestep of 4 fs and heavy hydrogens, using the charmm36 ff. Towards this end, I constructed the bilayer using Charmm-GUI and used pdb2gmx with the -heavyh flag to generate the appropriate topology. However when I use the grompp to generate the .tpr file, I get a warning: "Overriding atomtype OT". A quick look in the Charmm36 ffnonbonded.itp revealed that the atomtype OT corresponds to an oxygen with reduced atomic mass, which is perfectly understandable given the use of -heavyh flag. My problem is that I don't understand what the warning exactly means. A look at a previous gromacs thread where this "overriding atomtype" problem has been reported, didn't help. Is it safe to ignore this warning? In this case, yes, because the atom type overriding the previous instance has the same LJ parameters, just a different mass. When I ignored the warning and carried out a simple NVE run, it gave me potential, kinetic and total energies that were not conserved. Please find the plot of the energies and the associated NVE run parameters at this link https://drive.google.com/file/d/0B2cmuCsErAPZcjhmNW1tWnA3UXM/view?usp=sharing. A look at the trajectory in VMD revealed that the molecules which were initially very dynamic, start "freezing" as the KE approaches zero. Does anybody has any idea as to where I am going wrong? I would not expect any simulation with a 4-fs time step, mixed precision, constraints, etc. to conserve energy well under NVE. But the time you're showing here is totally inadequate to evaluate conservation of energy, anyway. Normally one would equilibrate for some time under NVT, then switch to NVE. This issue gets discussed all the time on the list, so check the archive for recent commentary. -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] Building gromacs 5.1.1: doesn't build all programs like grompp
On 11/19/15 10:26 AM, Stephen Cousins wrote: Hi, I'm trying to build gromacs and I have used the instructions as best as I can but I can never get programs like grompp to build. Here is what I'm doing: mkdir build cd build cmake .. -DGMX_X11=OFF -DCMAKE_INSTALL_PREFIX=/opt/centos7/gromacs/5.1.1-openmpi-gnu -DBUILD_SHARED_LIBS=OFF -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=OFF -DGMX_MPI=OFF -DGMX_BUILD_MDRUN_ONLY=ON make -j 10 all make install This makes mdrun. If I take off the last switch then it also builds gmx and templates. Here is what I get in the bin directory: -rwxr-xr-x 1 root root 3378 Jun 22 09:17 demux.pl -rwxr-xr-x 1 root root 18037512 Nov 17 01:16 gmx -rw-r--r-- 1 root root 149710 Nov 9 06:04 gmx-completion.bash -rw-r--r-- 1 root root 37 Nov 17 01:13 gmx-completion-gmx.bash -rw-r--r-- 1 root root 41 Nov 17 17:49 gmx-completion-gmx_mpi.bash -rw-r--r-- 1 root root 45 Nov 17 17:57 gmx-completion-mdrun.bash -rw-r--r-- 1 root root 49 Nov 17 17:54 gmx-completion-mdrun_mpi.bash -rwxr-xr-x 1 root root 17703540 Nov 17 17:53 gmx_mpi -rwxr-xr-x 1 root root 606 Nov 17 17:49 GMXRC -rwxr-xr-x 1 root root 2764 Nov 17 17:49 GMXRC.bash -rwxr-xr-x 1 root root 3015 Nov 17 17:49 GMXRC.csh -rwxr-xr-x 1 root root 138 Nov 17 17:49 GMXRC.zsh -rwxr-xr-x 1 root root 12481020 Nov 17 17:58 mdrun -rwxr-xr-x 1 root root 12541049 Nov 17 17:55 mdrun_mpi -rwxr-xr-x 1 root root 8217 Jun 22 09:17 xplor2gmx.pl This is after turning MPI on too. In an older system when I did this I got over 200 programs. Can you please help me figure out what I'm doing wrong? Nothing. There is only a gmx binary in the latest version. gmx grompp ... gmx pdb2gmx ... -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] Building gromacs 5.1.1: doesn't build all programs like grompp
Hi, I'm trying to build gromacs and I have used the instructions as best as I can but I can never get programs like grompp to build. Here is what I'm doing: mkdir build cd build cmake .. -DGMX_X11=OFF -DCMAKE_INSTALL_PREFIX=/opt/centos7/gromacs/5.1.1-openmpi-gnu -DBUILD_SHARED_LIBS=OFF -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=OFF -DGMX_MPI=OFF -DGMX_BUILD_MDRUN_ONLY=ON make -j 10 all make install This makes mdrun. If I take off the last switch then it also builds gmx and templates. Here is what I get in the bin directory: -rwxr-xr-x 1 root root 3378 Jun 22 09:17 demux.pl -rwxr-xr-x 1 root root 18037512 Nov 17 01:16 gmx -rw-r--r-- 1 root root 149710 Nov 9 06:04 gmx-completion.bash -rw-r--r-- 1 root root 37 Nov 17 01:13 gmx-completion-gmx.bash -rw-r--r-- 1 root root 41 Nov 17 17:49 gmx-completion-gmx_mpi.bash -rw-r--r-- 1 root root 45 Nov 17 17:57 gmx-completion-mdrun.bash -rw-r--r-- 1 root root 49 Nov 17 17:54 gmx-completion-mdrun_mpi.bash -rwxr-xr-x 1 root root 17703540 Nov 17 17:53 gmx_mpi -rwxr-xr-x 1 root root 606 Nov 17 17:49 GMXRC -rwxr-xr-x 1 root root 2764 Nov 17 17:49 GMXRC.bash -rwxr-xr-x 1 root root 3015 Nov 17 17:49 GMXRC.csh -rwxr-xr-x 1 root root 138 Nov 17 17:49 GMXRC.zsh -rwxr-xr-x 1 root root 12481020 Nov 17 17:58 mdrun -rwxr-xr-x 1 root root 12541049 Nov 17 17:55 mdrun_mpi -rwxr-xr-x 1 root root 8217 Jun 22 09:17 xplor2gmx.pl This is after turning MPI on too. In an older system when I did this I got over 200 programs. Can you please help me figure out what I'm doing wrong? Thanks, Steve -- Steve Cousins Supercomputer Engineer/Administrator Advanced Computing GroupUniversity of Maine System 244 Neville Hall (UMS Data Center) (207) 561-3574 Orono ME 04469 steve.cousins at maine.edu -- 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] Running ultiple job in core?
I suggest you clarify what exactly you want to achieve and share concrete information log files, otherwise we all have to guess. BTW, why do you expect "similar speed" with two runs using half the CU resources and sharing a GPU compared to using a single run that does not share the GPU (nor CPU with another)? -- Szilárd On Thu, Nov 19, 2015 at 3:45 AM, RJ wrote: > Hi there, > > > I have 24 threads in my PC with one GTX 980Ti GPU. I would like to run two > simulation job by assigning 12 threads for each job. I have tried using > "-ntomp 12 -ntmpi 1" for mentioning the threads and gpu. However, i couldnt > get the similar speed as if run them alone with 12 threads. I have even > used "-pin on" but haven't get any significant changes in the speed? > > > Its much appreciated if you could provide the hints on it. Thanks a lot. > -- > 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] Running ultiple job in core?
If you only have the one GPU, then both simulations will be trying to share the GPU resource, so they will not be able to obtain the same performance compared to running them separately. The only true solution is to use a second GPU. You may or may not find it useful to run one of your simulations with the GPU and one without, you can force a simulation to run CPU only by using: -nb CPU. Adam > On 19 Nov 2015, at 02:45, RJ wrote: > > Hi there, > > > I have 24 threads in my PC with one GTX 980Ti GPU. I would like to run two > simulation job by assigning 12 threads for each job. I have tried using > "-ntomp 12 -ntmpi 1" for mentioning the threads and gpu. However, i couldnt > get the similar speed as if run them alone with 12 threads. I have even used > "-pin on" but haven't get any significant changes in the speed? > > > Its much appreciated if you could provide the hints on it. Thanks a lot. > -- > 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. - We invite research leaders and ambitious early career researchers to join us in leading and driving research in key inter-disciplinary themes. Please see www.hw.ac.uk/researchleaders for further information and how to apply. Heriot-Watt University is a Scottish charity registered under charity number SC000278. -- 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] POPC simulation with heavy hydrogens and 4 fs timestep
Dear Gromacs Users, I have been trying to simulate a pure POPC bilayer with a timestep of 4 fs and heavy hydrogens, using the charmm36 ff. Towards this end, I constructed the bilayer using Charmm-GUI and used pdb2gmx with the -heavyh flag to generate the appropriate topology. However when I use the grompp to generate the .tpr file, I get a warning: "Overriding atomtype OT". A quick look in the Charmm36 ffnonbonded.itp revealed that the atomtype OT corresponds to an oxygen with reduced atomic mass, which is perfectly understandable given the use of -heavyh flag. My problem is that I don't understand what the warning exactly means. A look at a previous gromacs thread where this "overriding atomtype" problem has been reported, didn't help. Is it safe to ignore this warning? When I ignored the warning and carried out a simple NVE run, it gave me potential, kinetic and total energies that were not conserved. Please find the plot of the energies and the associated NVE run parameters at this link https://drive.google.com/file/d/0B2cmuCsErAPZcjhmNW1tWnA3UXM/view?usp=sharing. A look at the trajectory in VMD revealed that the molecules which were initially very dynamic, start "freezing" as the KE approaches zero. Does anybody has any idea as to where I am going wrong? 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.
Re: [gmx-users] surfactant.itp file
Please do not incessantly post the same question. I provided a suggestion yesterday for how to deal with that. If you want free help, you have to contribute by demonstrating a willingness to respond to suggestions. -Justin On 11/19/15 6:27 AM, mahdiyeh poorsargol wrote: -- Forwarded message -- From: mahdiyeh poorsargol Date: Thu, 19 Nov 2015 14:56:55 +0330 Subject: To: gmx-users Hello I'm a beginner in Gromacs and I want to work with the surfactant (for example SDS surfactant). I converted the surfactant.pdb file to the surfactant.itp file using TOPOLGEN, but for S atom, atomtype not defined! please help me. thankyou [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB . . 30 opls_136 1 LIG C 10 -0.120 12.01100 31 opls_140 1LIG H 10 0.0601.00800 32 opls_140 1LIG H 10 0.0601.00800 33 opls_136 1LIG C 11 -0.120 12.01100 34 opls_140 1LIG H 11 0.0601.00800 35 opls_140 1LIG H 11 0.0601.00800 36 opls_136 1LIG C 12 -0.120 12.01100 37 opls_140 1LIG H 12 0.0601.00800 38 opls_140 1LIG H 12 0.0601.00800 39 1 0 S 12 32 0.0000.0 40 opls_236 1LIG O 12 -0.500 15.99940 41 opls_154 1LIG O 12 -0.683 15.99940 42 opls_155 1LIG H 12 0.4181.00800 I have a OPLS-AA SDS, but I don't know how include in the TOPOLGEN! I use the command line: perl topolgen.pl -f input.pdb -o output.itp -type itp please help me! -- == 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] surfactant.itp file
-- Forwarded message -- From: mahdiyeh poorsargol Date: Thu, 19 Nov 2015 14:56:55 +0330 Subject: To: gmx-users Hello I'm a beginner in Gromacs and I want to work with the surfactant (for example SDS surfactant). I converted the surfactant.pdb file to the surfactant.itp file using TOPOLGEN, but for S atom, atomtype not defined! please help me. thankyou [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB . . 30 opls_136 1 LIG C 10 -0.120 12.01100 31 opls_140 1LIG H 10 0.0601.00800 32 opls_140 1LIG H 10 0.0601.00800 33 opls_136 1LIG C 11 -0.120 12.01100 34 opls_140 1LIG H 11 0.0601.00800 35 opls_140 1LIG H 11 0.0601.00800 36 opls_136 1LIG C 12 -0.120 12.01100 37 opls_140 1LIG H 12 0.0601.00800 38 opls_140 1LIG H 12 0.0601.00800 39 1 0 S 12 32 0.0000.0 40 opls_236 1LIG O 12 -0.500 15.99940 41 opls_154 1LIG O 12 -0.683 15.99940 42 opls_155 1LIG H 12 0.4181.00800 I have a OPLS-AA SDS, but I don't know how include in the TOPOLGEN! I use the command line: perl topolgen.pl -f input.pdb -o output.itp -type itp please help me! -- 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] (no subject)
Hello I'm a beginner in Gromacs and I want to work with the surfactant (for example SDS surfactant). I converted the surfactant.pdb file to the surfactant.itp file using TOPOLGEN, but for S atom, atomtype not defined! please help me. thankyou [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB . . 30 opls_136 1 LIG C 10 -0.120 12.01100 31 opls_140 1LIG H 10 0.0601.00800 32 opls_140 1LIG H 10 0.0601.00800 33 opls_136 1LIG C 11 -0.120 12.01100 34 opls_140 1LIG H 11 0.0601.00800 35 opls_140 1LIG H 11 0.0601.00800 36 opls_136 1LIG C 12 -0.120 12.01100 37 opls_140 1LIG H 12 0.0601.00800 38 opls_140 1LIG H 12 0.0601.00800 39 1 0 S 12 32 0.0000.0 40 opls_236 1LIG O 12 -0.500 15.99940 41 opls_154 1LIG O 12 -0.683 15.99940 42 opls_155 1LIG H 12 0.4181.00800 I have a OPLS-AA SDS, but I don't know how include in the TOPOLGEN! I use the command line: perl topolgen.pl -f input.pdb -o output.itp -type itp please help me! -- 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 5 and Shake
Dear Gromacs users, I wanted to perform a simulation with gromacs v.5, using shake algorithm to constraint bond lengths. Looking at the mdp options, shake method is still available, however, the particle decomposition algorithm has been dropped in gromacs 5, and shake seems not to be compatible with decomposition of the system in multiple domains. I was wondering if there is a way to perform simulations with shake on multiple threads. Every suggestion (related to the use of shake!) is welcome. Thank you in advance, Luigi -- 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] calculate apolar contact area
Hi, I want to calculate the apolar contacts area between a peptide and its receptor in the simulation by using g_sas, i.e.,the apolar surface area of the hydrophobic residues on the peptide that are buried by apolar surface area of the receptor. Now I can only get the surface area of hydrophobic residues on the peptide that are buried by the receptor: SASA1(without protein)-SASA2(with protein)=buried surface area. But I can't distinguish how much the hydrophobic parts of receptor and the hydrophilic parts of the receptor contributes to the buried area, respectively. I think the buried area contributed by the hydrophobic parts of receptor, rather than by the hydrophilic parts, is the real aplar contacts area,. Because when the surface area of hydrophobic residues on the peptide are buried by hydrophilic parts of the receptor,there are no apolar contacts. To solve the problem,I've tried to calculate the SASA of an index group comprising the peptide and the hydrophobic parts of the receptor(sidechain atoms of nonpolar residues and hydrophobic parts of other polar residues as well as all C-alpha atoms), the output SASA of the peptide is SASA3. So "SASA1(without protein)-SASA3(with hydrophobic parts of protein)" may be the apolar contacts area I need? But polar atoms (or the hydrophilic parts I definied) are missing in this calculation,this should affect the result ! Because some nonpolar atoms are buried by polar atoms in the receptor. So I'm confused whether there is a better way to obtain the apolar contact area. Thank you in advance! Best, Linlin Thanks & With best regards！ Linlin Yang | 杨琳琳 Drug Discovery and Design Center (DDDC) Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences (CAS) Tel：+86-21-50806600 ext.1201 Address:555 Zu Chong Zhi Road, Zhang Jiang Hi-Tech Park， Pudong District, Shanghai, 201203, P.R. China -- 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.
