Re: [gmx-users] Position restraining of ions.
You can copy the part regarding the certain ion type from ions.itp to a separate itp file and #include that itp file into a top file. Then #include the position restraint file that has restraints for only one ion of that type at the end of that new itp file. By this manner you can even split a group of same ions (for example, some potassium ions are restrained and others are not) by making separate itp files for potassium ions in which you specify different [ moleculetype ] names for each file and doing that accordingly at the [ molecules ] table at the end of a top file. Of course, when you split groups you need to know the positions of ions of interest in a system structural file (gro or pdb), as they need to be listed in the same order in the [ molecules ] table. Gordan On 7/16/2015 2:36 AM, Justin Lemkul wrote: On 7/15/15 11:53 AM, anu chandra wrote: Dear Gromcacs users, I have carried out 25 ns simulation of membrane-protein systems. Now, I would like to do position restrain of ions for the next 1-2 ns. I have KCl in my system. I used ' genrestr ' for generating the position restrain for ions using the following command - genrestr -f md50.gro -o ions-rest.itp I have included ions-rest.itp in the .top file with proper ' ifdef ' term as mention in tutorials. Unfortunately, the grommp shows error message - Atom index (2) in position_restraints out of bounds (1-1). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to . I have seen from Gromcas mail list that many faced similar issues and this usually comes from the mismatch in atom indices. Unfortunately, I could not find complete solution for it yet. Few queries in this regard are, 1. How can I generate a position restrain file for ions or any set of molecules in the system? my topology file have following hierarchy, ; This is a standalone topology file ; ; Created by: ; GROMACS: gmx pdb2gmx, VERSION 5.0.4 ; Executable: /usr/local/gromacs/bin/gmx ; Library dir: /usr/local/gromacs/share/gromacs/top ; Command line: ; gmx pdb2gmx -f step5_IP3R.pdb -ter ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include charmm36-jun2015.ff/forcefield.itp ; Include chain topologies #include topol_Protein.itp #include topol_Protein2.itp #include topol_Protein3.itp #include topol_Protein4.itp #include POPC.itp ; Include water topology #include charmm36-jun2015.ff/tip3p.itp ; Include topology for ions #include charmm36-jun2015.ff/ions.itp [ system ] ; Name Titile [ molecules ] ; Compound#mols Protein 1 Protein21 Protein31 Protein41 POPC 295 POT 85 CL 122 SOL24892 2. Where all I can use the .itp file for a particular group generate with ' genrestr' command? Restraints are applied on a per-moleculetype basis; hence genrestr is very limited in what it can do (multiple molecules won't work without considerable effort). The only way to restrain the ions within this setup is to modify ions.itp to specify restraints within the relevant [moleculetype] directives. -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] Position restraining of ions.
Hi, Thanks for your prompt reply. I have modified the top file as shown below. Though it looks working fine for me, can you please have quick look into it. *** r ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include charmm36-jun2015.ff/forcefield.itp ; Include chain topologies #include topol_Protein.itp #include topol_Protein2.itp #include topol_Protein3.itp #include topol_Protein4.itp #include POPC.itp #include POT.itp #ifdef REST_ON #include POT_rest.itp #endif #include CL.itp #ifdef REST_ON #include CL_rest.itp #endif ; Include water topology #include charmm36-jun2015.ff/tip3p.itp [ system ] ; Name Titile [ molecules ] ; Compound#mols Protein 1 Protein21 Protein31 Protein41 POPC 295 POT 85 CL 122 SOL 24892 ** And my POT_rest.itp and CL_rest have similar format as follows, *** ; position restraints for POT of GROningen MAchine for Chemical Simulation [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 *** and I have ' define = -DREST_ON ' in mdp file. Hope what I am doing is right? Many thanks Anu On Thu, Jul 16, 2015 at 7:32 AM, Gordan Horvat ghor...@chem.pmf.hr wrote: You can copy the part regarding the certain ion type from ions.itp to a separate itp file and #include that itp file into a top file. Then #include the position restraint file that has restraints for only one ion of that type at the end of that new itp file. By this manner you can even split a group of same ions (for example, some potassium ions are restrained and others are not) by making separate itp files for potassium ions in which you specify different [ moleculetype ] names for each file and doing that accordingly at the [ molecules ] table at the end of a top file. Of course, when you split groups you need to know the positions of ions of interest in a system structural file (gro or pdb), as they need to be listed in the same order in the [ molecules ] table. Gordan On 7/16/2015 2:36 AM, Justin Lemkul wrote: On 7/15/15 11:53 AM, anu chandra wrote: Dear Gromcacs users, I have carried out 25 ns simulation of membrane-protein systems. Now, I would like to do position restrain of ions for the next 1-2 ns. I have KCl in my system. I used ' genrestr ' for generating the position restrain for ions using the following command - genrestr -f md50.gro -o ions-rest.itp I have included ions-rest.itp in the .top file with proper ' ifdef ' term as mention in tutorials. Unfortunately, the grommp shows error message - Atom index (2) in position_restraints out of bounds (1-1). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to . I have seen from Gromcas mail list that many faced similar issues and this usually comes from the mismatch in atom indices. Unfortunately, I could not find complete solution for it yet. Few queries in this regard are, 1. How can I generate a position restrain file for ions or any set of molecules in the system? my topology file have following hierarchy, ; This is a standalone topology file ; ; Created by: ; GROMACS: gmx pdb2gmx, VERSION 5.0.4 ; Executable: /usr/local/gromacs/bin/gmx ; Library dir: /usr/local/gromacs/share/gromacs/top ; Command line: ; gmx pdb2gmx -f step5_IP3R.pdb -ter ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include charmm36-jun2015.ff/forcefield.itp ; Include chain topologies #include topol_Protein.itp #include topol_Protein2.itp #include topol_Protein3.itp #include topol_Protein4.itp #include POPC.itp ; Include water topology #include charmm36-jun2015.ff/tip3p.itp ; Include topology for ions #include charmm36-jun2015.ff/ions.itp [ system ] ; Name Titile [ molecules ] ; Compound#mols Protein 1 Protein21 Protein31 Protein41 POPC 295 POT 85 CL 122 SOL24892 2. Where all I can use the .itp file for a particular group generate with ' genrestr' command? Restraints are applied on a per-moleculetype basis; hence genrestr is very limited in what it can do (multiple
Re: [gmx-users] Problem running equilibration step
Hi, The error is rather clear. There are atoms that are not coupled to any thermostat. In principle, you can set tc-grps to System and only give one tau and reference temperature and it will work. If you need a more elaborated scheme, them you can supply group definitions (if not available but default) with an index file. Felipe On 16/07/15 12:37, Priyanka Patel wrote: Dear all, I am doing simulation of DNA nano-structure using Gromacs (VERSION 4.6.5) by applying CHARMM26 force field and TIP4P water model. The energy minimization step is working fine but i am facing problem during equilibration step due to wrong *nvt.mdp* file. Can you please guide me, which kind of parameter should be change in *nvt.mdp* file for DNA nano-structure MD simulation. I am following Justin A. Lemkul's tutorial (Lysozyme in water) using following link; http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html I am getting error like this; Fatal error: 318 atoms are not part of any of the T-Coupling groups My command line is like this; *grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr * I am also attaching the modified nvt.mdp file according to DNA MD simulation requirement for your reference. I am working under the government organization, National center for Cell Science meant for non-profit research. I shall be highly obliged if you could help me to solve this problem. -- Felipe Merino Max Planck Institute for Molecular Physiology Department of Structural Biochemistry Otto-Hahn-Str. 11 44227 Dortmund Phone: +49 231 133 2306 -- 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] Problem running equilibration step
Dear all, I am doing simulation of DNA nano-structure using Gromacs (VERSION 4.6.5) by applying CHARMM26 force field and TIP4P water model. The energy minimization step is working fine but i am facing problem during equilibration step due to wrong *nvt.mdp* file. Can you please guide me, which kind of parameter should be change in *nvt.mdp* file for DNA nano-structure MD simulation. I am following Justin A. Lemkul's tutorial (Lysozyme in water) using following link; http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html I am getting error like this; Fatal error: 318 atoms are not part of any of the T-Coupling groups My command line is like this; *grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr * I am also attaching the modified nvt.mdp file according to DNA MD simulation requirement for your reference. I am working under the government organization, National center for Cell Science meant for non-profit research. I shall be highly obliged if you could help me to solve this problem. -- Regards, Priyanka Patel Mo:+91-8805811500 -- 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] Position restraining of ions.
#ifdef REST_ON #include POT_rest.itp #endif should go at the end of POT_rest.itp file and #ifdef REST_ON #include CL_rest.itp #endif should go at the end of CL.itp file. The restraint you listed restraints the first atom of every molecule of the type stated in the corresponding itp file. Since potassium and chloride ions are monoatomic, that should work fine. Elsewise, you can just put the line #include ionX_rest.itp at the end of the ionX.itp file which will turn on restraints automatically without having to define -DPOSIONX keyword in mdp file. Gordan On 7/16/2015 11:51 AM, anu chandra wrote: Hi, Thanks for your prompt reply. I have modified the top file as shown below. Though it looks working fine for me, can you please have quick look into it. *** r ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include charmm36-jun2015.ff/forcefield.itp ; Include chain topologies #include topol_Protein.itp #include topol_Protein2.itp #include topol_Protein3.itp #include topol_Protein4.itp #include POPC.itp #include POT.itp #ifdef REST_ON #include POT_rest.itp #endif #include CL.itp #ifdef REST_ON #include CL_rest.itp #endif ; Include water topology #include charmm36-jun2015.ff/tip3p.itp [ system ] ; Name Titile [ molecules ] ; Compound#mols Protein 1 Protein21 Protein31 Protein41 POPC 295 POT 85 CL 122 SOL 24892 ** And my POT_rest.itp and CL_rest have similar format as follows, *** ; position restraints for POT of GROningen MAchine for Chemical Simulation [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 *** and I have ' define = -DREST_ON ' in mdp file. Hope what I am doing is right? Many thanks Anu On Thu, Jul 16, 2015 at 7:32 AM, Gordan Horvat ghor...@chem.pmf.hr wrote: You can copy the part regarding the certain ion type from ions.itp to a separate itp file and #include that itp file into a top file. Then #include the position restraint file that has restraints for only one ion of that type at the end of that new itp file. By this manner you can even split a group of same ions (for example, some potassium ions are restrained and others are not) by making separate itp files for potassium ions in which you specify different [ moleculetype ] names for each file and doing that accordingly at the [ molecules ] table at the end of a top file. Of course, when you split groups you need to know the positions of ions of interest in a system structural file (gro or pdb), as they need to be listed in the same order in the [ molecules ] table. Gordan On 7/16/2015 2:36 AM, Justin Lemkul wrote: On 7/15/15 11:53 AM, anu chandra wrote: Dear Gromcacs users, I have carried out 25 ns simulation of membrane-protein systems. Now, I would like to do position restrain of ions for the next 1-2 ns. I have KCl in my system. I used ' genrestr ' for generating the position restrain for ions using the following command - genrestr -f md50.gro -o ions-rest.itp I have included ions-rest.itp in the .top file with proper ' ifdef ' term as mention in tutorials. Unfortunately, the grommp shows error message - Atom index (2) in position_restraints out of bounds (1-1). This probably means that you have inserted topology section position_restraints in a part belonging to a different molecule than you intended to . I have seen from Gromcas mail list that many faced similar issues and this usually comes from the mismatch in atom indices. Unfortunately, I could not find complete solution for it yet. Few queries in this regard are, 1. How can I generate a position restrain file for ions or any set of molecules in the system? my topology file have following hierarchy, ; This is a standalone topology file ; ; Created by: ; GROMACS: gmx pdb2gmx, VERSION 5.0.4 ; Executable: /usr/local/gromacs/bin/gmx ; Library dir: /usr/local/gromacs/share/gromacs/top ; Command line: ; gmx pdb2gmx -f step5_IP3R.pdb -ter ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include charmm36-jun2015.ff/forcefield.itp ; Include chain topologies #include topol_Protein.itp #include topol_Protein2.itp #include topol_Protein3.itp #include topol_Protein4.itp #include POPC.itp ; Include water topology #include charmm36-jun2015.ff/tip3p.itp ; Include topology for ions #include
[gmx-users] Analysis of the RMSF of a ligand bound protein structure
Dear all, I am performing MD simulation on a ligand bound dimeric protein structure in Gromacs 5.04. For the calculation of RMSF of this dimeric protein I have used the following command gmx rmsf -s md_0_1.tpr -f md_0_1_traj.xtc -res -o rmsf_res.xvgand selected 'C alpha' group. But the resulting plot shows graph corresponding to the ligand also. Is there any way to plot only the RMSF values of the dimeric protein without the bound ligand in gromacs? Will it be okay if I take the RMSF values of only the protein residues from rmsf_res.xvg and plot in any other graphical interface? Thanks and Regards,Paulami -- 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] Histogram result in free energy calculation
Dear GROMACS users. I have been studying free energy calculation in Justin tutorial. But, I got a somewhat different histogram result compared to the result in Justin tutorial. I uploaded my result files at the following link: http://bio.gnu.ac.kr/~chip/ I don't know why the result is different. Please give me some advice about this issue. Regards, Minky, -- 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 running equilibration step
Hello Felipe, Thanks for quick response, I have change my nvt.mdp file according to your instruction, but still getting the following error; Fatal error: Invalid T coupling input: 1 groups, 2 ref-t values and 2 tau-t values Priyanka On Thu, Jul 16, 2015 at 4:15 PM, Felipe Merino felipe.mer...@mpi-dortmund.mpg.de wrote: Hi, The error is rather clear. There are atoms that are not coupled to any thermostat. In principle, you can set tc-grps to System and only give one tau and reference temperature and it will work. If you need a more elaborated scheme, them you can supply group definitions (if not available but default) with an index file. Felipe On 16/07/15 12:37, Priyanka Patel wrote: Dear all, I am doing simulation of DNA nano-structure using Gromacs (VERSION 4.6.5) by applying CHARMM26 force field and TIP4P water model. The energy minimization step is working fine but i am facing problem during equilibration step due to wrong *nvt.mdp* file. Can you please guide me, which kind of parameter should be change in *nvt.mdp* file for DNA nano-structure MD simulation. I am following Justin A. Lemkul's tutorial (Lysozyme in water) using following link; http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html I am getting error like this; Fatal error: 318 atoms are not part of any of the T-Coupling groups My command line is like this; *grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr * I am also attaching the modified nvt.mdp file according to DNA MD simulation requirement for your reference. I am working under the government organization, National center for Cell Science meant for non-profit research. I shall be highly obliged if you could help me to solve this problem. -- Felipe Merino Max Planck Institute for Molecular Physiology Department of Structural Biochemistry Otto-Hahn-Str. 11 44227 Dortmund Phone: +49 231 133 2306 -- 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. -- Regards, Priyanka Patel Mo:+91-8805811500 -- 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 does x2top recognize between alkane C and alkene C
On 7/16/15 12:47 AM, sridhar dwadasi wrote: Thank you for the response. In case of an all atom representation, the connections are different. What about a united atom representation? The g_x2top supports Gromacs 53a5 forcefield right? If you write an .n2t file for it, sure. Can we get a topology with x2top only for an all atom representation? Or is there anyway to get it for gromos or opls ua ? No, it works with any force field for which an .n2t file exists. -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] Position restraining of ions.
On 7/16/15 6:22 AM, Gordan Horvat wrote: #ifdef REST_ON #include POT_rest.itp #endif should go at the end of POT_rest.itp file and #ifdef REST_ON #include CL_rest.itp #endif should go at the end of CL.itp file. The restraint you listed restraints the first atom of every molecule of the type stated in the corresponding itp file. Since potassium and chloride ions are monoatomic, that should work fine. Neither of the #ifdefs have to be in the actual .itp files. They must correspond to the [moleculetype], and since they are appropriately listed consecutively here, this approach works fine. Elsewise, you can just put the line #include ionX_rest.itp at the end of the ionX.itp file which will turn on restraints automatically without having to define -DPOSIONX keyword in mdp file. This is dangerous because then the restraints are *always* on, which is usually undesirable. If you forget to modify the files if conditions change, then run a long simulation... -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] LJ-14 energy
On 7/16/15 7:08 AM, Ming Tang wrote: Dear Justin, Thanks. 1. The total Lennar-Jones 12-6 energy of the whole system is the addition of LJ-14, LJ-SR and LJ-LR. Analogously, the coulomb energy is the addition of coulomb-14, coulomb-SR and coulomb-LR. Is my understanding of your explanation right? Besides, in Gromacs, is the potential energy the addition of G96Bond, G96Angle, Proper-Dih, Improper-Dih, LJ-14, Coulomb-14, LJ-SR, LJ-LR, Coulomb-SR and Coulomb-LR? You are right. That's why I don't Well, that's the exact definition of an additive functional form, so yes. get the LJ-LR and Coulomb-LR options when using g_energy. Suddenly, I realised that my understanding of the twin-range approach was totally wrong. For cutoff-scheme = verlet, rlist cannot be smaller than rvdw = rcoulomb, and When using twin-range method, either coulombtype = cut-off with rcoulomb ≥ rlist or vdwtype = cut-off with rvdw ≥ rlist. Does this mean that for twin-range approach, rlist = rcoulomb = rvdw when cutoff-scheme = verlet? However, even if I set vdw-modifier = potential- switch, the rlistlong larger than rlist is reset to be equal to rlist by gromacs, and there is not LJ-SR option when using g_energy. I am totally lost. Can you help to tell me how does twin-range work when cutoff-scheme = verlet? Another question is I used the following code to make my cut-off parameters be consistent with those used for the triple-range cut-off scheme in the paper defining Gromos 54a7 force field: coulombtype = reaction-field coulomb-modifier = potential-shift rcoulomb-switch = 0.8 rcoulomb = 1.4 epsilon_rf = 61 Currently, I think it is wrong. It seems that rlist = 0.8 is reasonable. But rlist should not be smaller than rcoulomb when cutoff-scheme = verlet. How to achieve this triple-range cut-off scheme? I honestly have no idea. I don't use GROMOS force fields any more. With the group scheme, it is easy, but with Verlet I have no idea what the equivalent approach is. 2. The pull rate I use is 4e-5/ps. I thought it is small so that the energy of water can be treated as constant during the pull process. I forgot to consider the water-protein interaction and that my pull rate is much larger than the pull rates used in the experiments which is in order of micrometre per second and is much more relevant to physiological pulling rate. You are right, I cannot treat the trends of the system's energy as those of the protein's energy. But how can I get the energy of the protein? Is it feasible to set all the atoms of the protein as one energy group, and do rerun to achieve this? The energy of the protein is not a useful quantity. It is a force field-specific quantity. Energy differences and free energies are valuable. -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] Position restraining of ions.
I should correct myself. Your top file should work too, because grompp assigns certain restraints included in top file to molecules of type defined in the first itp file found above the line that includes these restraints. http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds Alternatively, you can put the #ifdef REST_ON [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif section in your top file below the line that includes the ion group itp file, or in the itp file of each ion group you want restrained. Gordan On 7/16/2015 13:47 PM, Justin Lemkul wrote: On 7/16/15 6:22 AM, Gordan Horvat wrote: #ifdef REST_ON #include POT_rest.itp #endif should go at the end of POT_rest.itp file and #ifdef REST_ON #include CL_rest.itp #endif should go at the end of CL.itp file. The restraint you listed restraints the first atom of every molecule of the type stated in the corresponding itp file. Since potassium and chloride ions are monoatomic, that should work fine. Neither of the #ifdefs have to be in the actual .itp files. They must correspond to the [moleculetype], and since they are appropriately listed consecutively here, this approach works fine. Elsewise, you can just put the line #include ionX_rest.itp at the end of the ionX.itp file which will turn on restraints automatically without having to define -DPOSIONX keyword in mdp file. This is dangerous because then the restraints are *always* on, which is usually undesirable. If you forget to modify the files if conditions change, then run a long simulation... -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] LJ-14 energy
Dear Justin, Thanks. 1. The total Lennar-Jones 12-6 energy of the whole system is the addition of LJ-14, LJ-SR and LJ-LR. Analogously, the coulomb energy is the addition of coulomb-14, coulomb-SR and coulomb-LR. Is my understanding of your explanation right? Besides, in Gromacs, is the potential energy the addition of G96Bond, G96Angle, Proper-Dih, Improper-Dih, LJ-14, Coulomb-14, LJ-SR, LJ-LR, Coulomb-SR and Coulomb-LR? You are right. That's why I don't get the LJ-LR and Coulomb-LR options when using g_energy. Suddenly, I realised that my understanding of the twin-range approach was totally wrong. For cutoff-scheme = verlet, rlist cannot be smaller than rvdw = rcoulomb, and When using twin-range method, either coulombtype = cut-off with rcoulomb ≥ rlist or vdwtype = cut-off with rvdw ≥ rlist. Does this mean that for twin-range approach, rlist = rcoulomb = rvdw when cutoff-scheme = verlet? However, even if I set vdw-modifier = potential- switch, the rlistlong larger than rlist is reset to be equal to rlist by gromacs, and there is not LJ-SR option when using g_energy. I am totally lost. Can you help to tell me how does twin-range work when cutoff-scheme = verlet? Another question is I used the following code to make my cut-off parameters be consistent with those used for the triple-range cut-off scheme in the paper defining Gromos 54a7 force field: coulombtype = reaction-field coulomb-modifier = potential-shift rcoulomb-switch = 0.8 rcoulomb = 1.4 epsilon_rf = 61 Currently, I think it is wrong. It seems that rlist = 0.8 is reasonable. But rlist should not be smaller than rcoulomb when cutoff-scheme = verlet. How to achieve this triple-range cut-off scheme? 2. The pull rate I use is 4e-5/ps. I thought it is small so that the energy of water can be treated as constant during the pull process. I forgot to consider the water-protein interaction and that my pull rate is much larger than the pull rates used in the experiments which is in order of micrometre per second and is much more relevant to physiological pulling rate. You are right, I cannot treat the trends of the system's energy as those of the protein's energy. But how can I get the energy of the protein? Is it feasible to set all the atoms of the protein as one energy group, and do rerun to achieve this? Thanks, Regards -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Thursday, 16 July 2015 11:20 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] LJ-14 energy On 7/15/15 8:39 PM, Ming Tang wrote: Dear Chaban and Justin, Sorry for the mis-action. Please ignore my last email. Thank you both for your free help. I am pulling a collagen triple helix in a periodic water box using umbrella direction-periodic. I want to calculate the Lennard-Jones 12-6 of the protein. According to Gromacs manual, it contains repulsive short-range term and attractive long-range term. Is the Lennard-Jones 12-6 energy simply the addition of LJ-SR and LJ-LR? I am interested in the energy trends more than LJ-LR only exists with a twin-range cutoff approach. The total LJ between any groups also includes LJ-14 for intramolecular terms. Intermolecular LJ would be the sum of LJ-SR and LJ-LR, if the latter exists. the energy absolute values. So, if I can calculate the LJ 12-6 of the whole system, it is fine, because I can assume the energy of the water is not subject to change due to pulling. Why can you assume that? You're pulling a structure, which is a non-equilibrium process. There will be different interactions as a function of time. Water-water interactions at long distance from the protein indeed are unlikely to be affected, but those close to the protein may be different (though electrostatics/hydrogen bonding are probably much more interesting). Water-protein interactions certainly can't be assumed to be unchanging during pulling. -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
Re: [gmx-users] Histogram result in free energy calculation
On 7/16/15 3:02 AM, minky son wrote: Dear GROMACS users. I have been studying free energy calculation in Justin tutorial. But, I got a somewhat different histogram result compared to the result in Justin tutorial. I uploaded my result files at the following link: http://bio.gnu.ac.kr/~chip/ The website doesn't load. I don't know why the result is different. Note that the histograms I provide in the tutorial are parsed from the raw (and very convoluted) output that gmx bar gives. You would have to do the same separation of data sets to produce those plots, otherwise they will look wildly different. Also note that you shouldn't expect to reproduce the plots exactly (like any simulation, there is randomness) but the final free energy values should be very robust and absolutely reproducible (I've repeated it several times, across multiple GROMACS versions). -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] Problem running equilibration step
On 7/16/15 7:35 AM, Priyanka Patel wrote: Hello Felipe, Thanks for quick response, I have change my nvt.mdp file according to your instruction, but still getting the following error; Fatal error: Invalid T coupling input: 1 groups, 2 ref-t values and 2 tau-t values Again, the error is rather obvious. You have one group and you're trying to set up two thermostat reference and relaxation values. Also note that you should not use the tutorial's settings (which are for OPLS) when using the CHARMM force field. Those settings are at http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM -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] Position restraining of ions.
Thanks for the reply. I have one more quick query about position restrain here and its about restraining some pat of the whole protein. Say, I have a protein of 400 aminoacinds ( ie., residues no. 1-400). I would like to set up position restrain in such way that backbone atoms of residues 101-200 and 301-400 assign a fixed restrain force of 1000 KJ through-out the equilibration process and rest of the atoms ( ie, sidechain atoms of 101-200 and 301-400 and all atoms of residues 1-100 and 201-300) have descending order of restrain force starting with 1000 KJ, then 500 KJ, followed by 100 KJ, 50 KJ and finally, 0 KJ. How can I generate such a position restrain file in Gromcas? Many thanks in advance Anu On Thu, Jul 16, 2015 at 1:38 PM, Gordan Horvat ghor...@chem.pmf.hr wrote: I should correct myself. Your top file should work too, because grompp assigns certain restraints included in top file to molecules of type defined in the first itp file found above the line that includes these restraints. http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds Alternatively, you can put the #ifdef REST_ON [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif section in your top file below the line that includes the ion group itp file, or in the itp file of each ion group you want restrained. Gordan On 7/16/2015 13:47 PM, Justin Lemkul wrote: On 7/16/15 6:22 AM, Gordan Horvat wrote: #ifdef REST_ON #include POT_rest.itp #endif should go at the end of POT_rest.itp file and #ifdef REST_ON #include CL_rest.itp #endif should go at the end of CL.itp file. The restraint you listed restraints the first atom of every molecule of the type stated in the corresponding itp file. Since potassium and chloride ions are monoatomic, that should work fine. Neither of the #ifdefs have to be in the actual .itp files. They must correspond to the [moleculetype], and since they are appropriately listed consecutively here, this approach works fine. Elsewise, you can just put the line #include ionX_rest.itp at the end of the ionX.itp file which will turn on restraints automatically without having to define -DPOSIONX keyword in mdp file. This is dangerous because then the restraints are *always* on, which is usually undesirable. If you forget to modify the files if conditions change, then run a long simulation... -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. -- 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] gmx hydorder
Hi gromacs users, I want to use gmx hydorder to get the local tetrahedral arrangement of water surrounding protein within .1 nm . If I understand correctly from this paper in the gromacs manual (P.-L. Chau and A.J. Hardwick, Mol. Phys., 93, (1998)) I think I should get tetrahedrality for each frame as a function of time. I am having difficulty understanding the output in this case .xpm and file1 and file 2 (see my input below). gmx hydorder -s md_0_1.tpr -f npt.gro -o hydorder_test.xpm hydorder_test2.xpm -n index_water_prot.ndx -or file1 file2 Thank you for the help! Jessica -- -- 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] g_covar Segmentation fault problem
Dear gromacs user, In order to estimate system absolute entropy value I want to use g_covar + g_anaeig commands. However when I *'g_covar -f nvt.trr -s nvt.tpr'* I get a segmentation fault after *'Diagonalizing '* step from gromacs 4.6.6 and 5.0.3. *Constructing covariance matrix (12258x12258) ...Last frame 4000 time 4000.000 Read 4001 framesTrace of the covariance matrix: 12454.6 (nm^2)Diagonalizing ...Sum of the eigenvalues: 12454.6 (nm^2)Segmentation fault (core dumped)* But the same command, executed with g_covar of gromacs 4.6.3 works without any error or fault. Was it a bug and corrected for newer versions? I saw the release note of * 'Fixed a complicated bug in g_anaeig and g_covar, if the number of frames for a covariance analysis is fewer than the number of degrees of freedom' *for gromacs 4.6.6. Do I need to lower the number of atoms to analyze or higher the frame numbers or is it ok if I use 4.6.3? Thanks. -- 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] solvation free energy
I'm trying to calculate the solvation free energy of a molecule (M). I have done: M+water --- dum+water Now I have to do: M(vacuo) -- dum(vacuo) In this case I have a problem, in fact I find a DG = 0.0 and within the .xvg file there are only zeros. Where is the problem? I use gromacs 5.0.4 and my .mdp file (for lambda 00) is: integrator = sd tinit= 0 dt = 0.002 nsteps = 250 comm_mode= angular nstcomm = 100 nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstenergy= 500 nstxout-compressed = 0 cutoff-scheme= group nstlist = 0 ns_type = simple pbc = no rlist= 0 coulombtype = cutoff rcoulomb = 0 epsilon_r= 1 vdwtype = cutoff rvdw = 0 DispCorr = no fourierspacing = 0.12 pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 tcoupl = berendsen tc_grps = system tau_t= 0.1 ref_t= 300 Pcoupl = no tau_p= 1.0 compressibility = 4.5e-05 ref_p= 1.0 free_energy = yes init_lambda_state= 0 delta_lambda = 0 calc_lambda_neighbors= 1 vdw_lambdas = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00 coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 bonded_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 restraint_lambdas= 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 sc-alpha = 0.5 sc-coul = no sc-power = 1.0 sc-sigma = 0.3 couple-moltype = QUI couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no nstdhdl = 10 gen_vel = no constraints = all-bonds ; we only have C-H bonds here constraint-algorithm = lincs continuation = no lincs-order = 12 Best regards Daniele Veclani. -- 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] solvation free energy
The couple-* parameters take already care of including the non-bonded terms internal to your molecule to correctly describe the transfer of M to vacuum. That's the point of those parameters so that you would not have to run an additional correction in vacuo. See the discussion in the manual (it's section 5.3 for Gromacs 4.6.x). You would also need to compute the electrostatic transformation. On Thu, 16 Jul 2015 16:26:44 +0200 Daniele Veclani danielevecl...@gmail.com wrote: I'm trying to calculate the solvation free energy of a molecule (M). I have done: M+water --- dum+water Now I have to do: M(vacuo) -- dum(vacuo) In this case I have a problem, in fact I find a DG = 0.0 and within the .xvg file there are only zeros. Where is the problem? I use gromacs 5.0.4 and my .mdp file (for lambda 00) is: integrator = sd tinit= 0 dt = 0.002 nsteps = 250 comm_mode= angular nstcomm = 100 nstxout = 500 nstvout = 500 nstfout = 0 nstlog = 500 nstenergy= 500 nstxout-compressed = 0 cutoff-scheme= group nstlist = 0 ns_type = simple pbc = no rlist= 0 coulombtype = cutoff rcoulomb = 0 epsilon_r= 1 vdwtype = cutoff rvdw = 0 DispCorr = no fourierspacing = 0.12 pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 tcoupl = berendsen tc_grps = system tau_t= 0.1 ref_t= 300 Pcoupl = no tau_p= 1.0 compressibility = 4.5e-05 ref_p= 1.0 free_energy = yes init_lambda_state= 0 delta_lambda = 0 calc_lambda_neighbors= 1 vdw_lambdas = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00 coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 bonded_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 restraint_lambdas= 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 sc-alpha = 0.5 sc-coul = no sc-power = 1.0 sc-sigma = 0.3 couple-moltype = QUI couple-lambda0 = vdw couple-lambda1 = none couple-intramol = no nstdhdl = 10 gen_vel = no constraints = all-bonds ; we only have C-H bonds here constraint-algorithm = lincs continuation = no lincs-order = 12 Best regards Daniele Veclani. -- 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] Intel MKL taken in preference of the specified FFT library
Hi, I just downloaded Gromacs 5.1-rc1 and want to compile it using the GNU compilers and a self compiled FFTW*. I configured Gromacs with: $ cmake .. -DCMAKE_INSTALL_PREFIX=/home/reuti/local/gromacs-5.1-rc1 -DGMX_FFT_LIBRARY=fftw3 -DCMAKE_PREFIX_PATH=/home/reuti/local/fftw-3.3.4 As there was now shared version of FFTW it complains about it, and hence I compiled FFTW again - this time with shared library flag and the configure step of Gromacs succeeded. But after `make` and `make install` I faced the result, that the binary `gmx` like the library in lib64 were linked against Intel MKL. Well, there is an old version of the Intel MKL on the system and hence in the LD_LIBRARY_PATH. Once I cleared the LD_LIBRARY_PATH I got the result I expected. Question: is this the intended behavior? IMO the GMX_FFT_LIBRARY=fftw3 flag should be honored first and any set LD_LIBRARY_PATH ignored. -- Reuti *) The automatic download (like outlined in the INSTALL: -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON) of FFTW and the regression tests points to the Gromacs site, but AFAICS they were moved to box.com, hence the automatic download fails. -- 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 does x2top recognize between alkane C and alkene C
Hi Dr. Justin Lemkul, Thank you for responding again. I'm still not understanding it :(. I'll try to be more clear. Taking the example of OPLS UA, we have different atom types for united alkene atoms (-CH= and CH2=) and alkanes (-CH2-). When I represent the connections in n2t file, the -CH2- and -CH= will have two connections each. and the distances with other united carbons are 0.154nm and 0.140 nm as I have mentioned before. I have been giving the same information in the .n2t file. Based on the order in which they appear in the .n2t file, the atom appearing first is being taken by x2top to create the topology. I hope I made my problem clear. I'm unable to post my .n2t file now as I do not have it with me at the moment. If required I can post it tomorrow. Thanks and Regards Sridhar -- 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_covar Segmentation fault problem
On 7/16/15 12:26 PM, gozde ergin wrote: Thank for reply Justin but I have difficulty to understand which version has this bug? If 'Segmentation fault because of #DOF and frames numbers difference' is a bug than gromacs 4.6.3 is working correctly, right? Offhand, I don't know which outdated versions work and which don't. To be safe: 4.6.x series, use version = 4.6.6 5.0.x series, use version 5.0.5 Any other version in the development repo (master, release-5-0, etc) -Justin On Thu, Jul 16, 2015 at 6:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/16/15 10:22 AM, gozde ergin wrote: Dear gromacs user, In order to estimate system absolute entropy value I want to use g_covar + g_anaeig commands. However when I *'g_covar -f nvt.trr -s nvt.tpr'* I get a segmentation fault after *'Diagonalizing '* step from gromacs 4.6.6 and 5.0.3. *Constructing covariance matrix (12258x12258) ...Last frame 4000 time 4000.000 Read 4001 framesTrace of the covariance matrix: 12454.6 (nm^2)Diagonalizing ...Sum of the eigenvalues: 12454.6 (nm^2)Segmentation fault (core dumped)* But the same command, executed with g_covar of gromacs 4.6.3 works without any error or fault. Was it a bug and corrected for newer versions? I saw the release note of * 'Fixed a complicated bug in g_anaeig and g_covar, if the number of frames for a covariance analysis is fewer than the number of degrees of freedom' *for gromacs 4.6.6. The bug was also fixed for 5.0.5. -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. -- == 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] How does x2top recognize between alkane C and alkene C
On 7/16/15 12:57 PM, sridhar dwadasi wrote: Hi Dr. Justin Lemkul, Thank you for responding again. I'm still not understanding it :(. I'll try to be more clear. Taking the example of OPLS UA, we have different atom types for united alkene atoms (-CH= and CH2=) and alkanes (-CH2-). When I represent the connections in n2t file, the -CH2- and -CH= will have two connections each. and the distances with other united carbons are 0.154nm and 0.140 nm as I have mentioned before. I have been giving the same information in the .n2t file. Based on the order in which they appear in the .n2t file, the atom appearing first is being taken by x2top to create the topology. I hope I made my problem clear. I'm unable to post my .n2t file now as I do not have it with me at the moment. If required I can post it tomorrow. Yes, please post the .n2t file. Just keep in mind that x2top is a very simplistic program; you may have to play some tricks to get such a subtle distinction to work correctly. UA models will be particularly tricky because there won't necessarily be any H to distinguish different forms. You may have to either play with the specified bond length (putting one outside of the 10% tolerance of the other) or re-compile the code after modifying the allowable tolerance. In this case, 10% may be too permissive. -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] g_covar Segmentation fault problem
Ok by using version 4.6.6 I got this segmentation fault error which means number of frames should be equal or bigger than the number of degrees of freedom. On Thu, Jul 16, 2015 at 7:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/16/15 12:26 PM, gozde ergin wrote: Thank for reply Justin but I have difficulty to understand which version has this bug? If 'Segmentation fault because of #DOF and frames numbers difference' is a bug than gromacs 4.6.3 is working correctly, right? Offhand, I don't know which outdated versions work and which don't. To be safe: 4.6.x series, use version = 4.6.6 5.0.x series, use version 5.0.5 Any other version in the development repo (master, release-5-0, etc) -Justin On Thu, Jul 16, 2015 at 6:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/16/15 10:22 AM, gozde ergin wrote: Dear gromacs user, In order to estimate system absolute entropy value I want to use g_covar + g_anaeig commands. However when I *'g_covar -f nvt.trr -s nvt.tpr'* I get a segmentation fault after *'Diagonalizing '* step from gromacs 4.6.6 and 5.0.3. *Constructing covariance matrix (12258x12258) ...Last frame 4000 time 4000.000 Read 4001 framesTrace of the covariance matrix: 12454.6 (nm^2)Diagonalizing ...Sum of the eigenvalues: 12454.6 (nm^2)Segmentation fault (core dumped)* But the same command, executed with g_covar of gromacs 4.6.3 works without any error or fault. Was it a bug and corrected for newer versions? I saw the release note of * 'Fixed a complicated bug in g_anaeig and g_covar, if the number of frames for a covariance analysis is fewer than the number of degrees of freedom' *for gromacs 4.6.6. The bug was also fixed for 5.0.5. -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. -- == 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] g_covar Segmentation fault problem
On 7/16/15 1:09 PM, gozde ergin wrote: Ok by using version 4.6.6 I got this segmentation fault error which means number of frames should be equal or bigger than the number of degrees of freedom. Then use 4.6.7. Maybe my = should have been instead. The best bet when you get failures like this is to always upgrade to the latest version in whatever series you're trying to use. 4.6.7 should work. If not, 5.0.5 definitely does. -Justin On Thu, Jul 16, 2015 at 7:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/16/15 12:26 PM, gozde ergin wrote: Thank for reply Justin but I have difficulty to understand which version has this bug? If 'Segmentation fault because of #DOF and frames numbers difference' is a bug than gromacs 4.6.3 is working correctly, right? Offhand, I don't know which outdated versions work and which don't. To be safe: 4.6.x series, use version = 4.6.6 5.0.x series, use version 5.0.5 Any other version in the development repo (master, release-5-0, etc) -Justin On Thu, Jul 16, 2015 at 6:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/16/15 10:22 AM, gozde ergin wrote: Dear gromacs user, In order to estimate system absolute entropy value I want to use g_covar + g_anaeig commands. However when I *'g_covar -f nvt.trr -s nvt.tpr'* I get a segmentation fault after *'Diagonalizing '* step from gromacs 4.6.6 and 5.0.3. *Constructing covariance matrix (12258x12258) ...Last frame 4000 time 4000.000 Read 4001 framesTrace of the covariance matrix: 12454.6 (nm^2)Diagonalizing ...Sum of the eigenvalues: 12454.6 (nm^2)Segmentation fault (core dumped)* But the same command, executed with g_covar of gromacs 4.6.3 works without any error or fault. Was it a bug and corrected for newer versions? I saw the release note of * 'Fixed a complicated bug in g_anaeig and g_covar, if the number of frames for a covariance analysis is fewer than the number of degrees of freedom' *for gromacs 4.6.6. The bug was also fixed for 5.0.5. -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. -- == 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. -- == 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] g_covar Segmentation fault problem
Thank for reply Justin but I have difficulty to understand which version has this bug? If 'Segmentation fault because of #DOF and frames numbers difference' is a bug than gromacs 4.6.3 is working correctly, right? On Thu, Jul 16, 2015 at 6:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/16/15 10:22 AM, gozde ergin wrote: Dear gromacs user, In order to estimate system absolute entropy value I want to use g_covar + g_anaeig commands. However when I *'g_covar -f nvt.trr -s nvt.tpr'* I get a segmentation fault after *'Diagonalizing '* step from gromacs 4.6.6 and 5.0.3. *Constructing covariance matrix (12258x12258) ...Last frame 4000 time 4000.000 Read 4001 framesTrace of the covariance matrix: 12454.6 (nm^2)Diagonalizing ...Sum of the eigenvalues: 12454.6 (nm^2)Segmentation fault (core dumped)* But the same command, executed with g_covar of gromacs 4.6.3 works without any error or fault. Was it a bug and corrected for newer versions? I saw the release note of * 'Fixed a complicated bug in g_anaeig and g_covar, if the number of frames for a covariance analysis is fewer than the number of degrees of freedom' *for gromacs 4.6.6. The bug was also fixed for 5.0.5. -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] Position restraining of ions.
On 7/16/15 9:37 AM, anu chandra wrote: Thanks for the reply. I have one more quick query about position restrain here and its about restraining some pat of the whole protein. Say, I have a protein of 400 aminoacinds ( ie., residues no. 1-400). I would like to set up position restrain in such way that backbone atoms of residues 101-200 and 301-400 assign a fixed restrain force of 1000 KJ through-out the equilibration process and rest of the atoms ( ie, sidechain atoms of 101-200 and 301-400 and all atoms of residues 1-100 and 201-300) have descending order of restrain force starting with 1000 KJ, then 500 KJ, followed by 100 KJ, 50 KJ and finally, 0 KJ. How can I generate such a position restrain file in Gromcas? It can't be done with a single restraint file, but you can conditionally trigger different force constants. This is actually what CHARMM-GUI does to equilibrate the lipids, so look at the same logic. Create multiple restraint .itp files with genrestr and suitable index groups. -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] g_covar Segmentation fault problem
On 7/16/15 10:22 AM, gozde ergin wrote: Dear gromacs user, In order to estimate system absolute entropy value I want to use g_covar + g_anaeig commands. However when I *'g_covar -f nvt.trr -s nvt.tpr'* I get a segmentation fault after *'Diagonalizing '* step from gromacs 4.6.6 and 5.0.3. *Constructing covariance matrix (12258x12258) ...Last frame 4000 time 4000.000 Read 4001 framesTrace of the covariance matrix: 12454.6 (nm^2)Diagonalizing ...Sum of the eigenvalues: 12454.6 (nm^2)Segmentation fault (core dumped)* But the same command, executed with g_covar of gromacs 4.6.3 works without any error or fault. Was it a bug and corrected for newer versions? I saw the release note of * 'Fixed a complicated bug in g_anaeig and g_covar, if the number of frames for a covariance analysis is fewer than the number of degrees of freedom' *for gromacs 4.6.6. The bug was also fixed for 5.0.5. -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] LJ-14 energy
On Thu, Jul 16, 2015 at 1:24 PM Ming Tang m21.t...@qut.edu.au wrote: Dear Justin, Thanks. 1. The total Lennar-Jones 12-6 energy of the whole system is the addition of LJ-14, LJ-SR and LJ-LR. Analogously, the coulomb energy is the addition of coulomb-14, coulomb-SR and coulomb-LR. Is my understanding of your explanation right? Besides, in Gromacs, is the potential energy the addition of G96Bond, G96Angle, Proper-Dih, Improper-Dih, LJ-14, Coulomb-14, LJ-SR, LJ-LR, Coulomb-SR and Coulomb-LR? You are right. That's why I don't get the LJ-LR and Coulomb-LR options when using g_energy. Suddenly, I realised that my understanding of the twin-range approach was totally wrong. For cutoff-scheme = verlet, rlist cannot be smaller than rvdw = rcoulomb, and When using twin-range method, either coulombtype = cut-off with rcoulomb ≥ rlist or vdwtype = cut-off with rvdw ≥ rlist. Does this mean that for twin-range approach, rlist = rcoulomb = rvdw when cutoff-scheme = verlet? However, even if I set vdw-modifier = potential- switch, the rlistlong larger than rlist is reset to be equal to rlist by gromacs, and there is not LJ-SR option when using g_energy. I am totally lost. Can you help to tell me how does twin-range work when cutoff-scheme = verlet? http://manual.gromacs.org/documentation/5.1-rc1/user-guide/cutoff-schemes.html (and equivalent docs for earlier versions) indicate that twin-range is not supported by the Verlet scheme. (Technically, it could be supported, and some forms of it are in fact used by the PME-tuning facility, but some of us are unconvinced of the technical merit of such forms, nor do we like the confusion created by how such group-scheme features are named and implemented in GROMACS. So, if there is ever support, it's likely to be from a clean slate, and after we remove the group scheme.) Another question is I used the following code to make my cut-off parameters be consistent with those used for the triple-range cut-off scheme in the paper defining Gromos 54a7 force field: coulombtype = reaction-field coulomb-modifier = potential-shift rcoulomb-switch = 0.8 rcoulomb = 1.4 epsilon_rf = 61 Currently, I think it is wrong. It seems that rlist = 0.8 is reasonable. But rlist should not be smaller than rcoulomb when cutoff-scheme = verlet. How to achieve this triple-range cut-off scheme? You can't. Mark 2. The pull rate I use is 4e-5/ps. I thought it is small so that the energy of water can be treated as constant during the pull process. I forgot to consider the water-protein interaction and that my pull rate is much larger than the pull rates used in the experiments which is in order of micrometre per second and is much more relevant to physiological pulling rate. You are right, I cannot treat the trends of the system's energy as those of the protein's energy. But how can I get the energy of the protein? Is it feasible to set all the atoms of the protein as one energy group, and do rerun to achieve this? Thanks, Regards -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Thursday, 16 July 2015 11:20 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] LJ-14 energy On 7/15/15 8:39 PM, Ming Tang wrote: Dear Chaban and Justin, Sorry for the mis-action. Please ignore my last email. Thank you both for your free help. I am pulling a collagen triple helix in a periodic water box using umbrella direction-periodic. I want to calculate the Lennard-Jones 12-6 of the protein. According to Gromacs manual, it contains repulsive short-range term and attractive long-range term. Is the Lennard-Jones 12-6 energy simply the addition of LJ-SR and LJ-LR? I am interested in the energy trends more than LJ-LR only exists with a twin-range cutoff approach. The total LJ between any groups also includes LJ-14 for intramolecular terms. Intermolecular LJ would be the sum of LJ-SR and LJ-LR, if the latter exists. the energy absolute values. So, if I can calculate the LJ 12-6 of the whole system, it is fine, because I can assume the energy of the water is not subject to change due to pulling. Why can you assume that? You're pulling a structure, which is a non-equilibrium process. There will be different interactions as a function of time. Water-water interactions at long distance from the protein indeed are unlikely to be affected, but those close to the protein may be different (though electrostatics/hydrogen bonding are probably much more interesting). Water-protein interactions certainly can't be assumed to be unchanging during pulling. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II,
Re: [gmx-users] Intel MKL taken in preference of the specified FFT library
Hi, On Thu, Jul 16, 2015 at 5:47 PM Reuti re...@staff.uni-marburg.de wrote: Hi, I just downloaded Gromacs 5.1-rc1 and want to compile it using the GNU compilers and a self compiled FFTW*. I configured Gromacs with: $ cmake .. -DCMAKE_INSTALL_PREFIX=/home/reuti/local/gromacs-5.1-rc1 -DGMX_FFT_LIBRARY=fftw3 -DCMAKE_PREFIX_PATH=/home/reuti/local/fftw-3.3.4 As there was now shared version of FFTW it complains about it, and hence I compiled FFTW again - this time with shared library flag and the configure step of Gromacs succeeded. But after `make` and `make install` I faced the result, that the binary `gmx` like the library in lib64 were linked against Intel MKL. Well, there is an old version of the Intel MKL on the system and hence in the LD_LIBRARY_PATH. Once I cleared the LD_LIBRARY_PATH I got the result I expected. Older MKL had a feature of providing headers that look like FFTW but execute MKL, and programs will find that if it precedes real FFTW in the lookup path. Question: is this the intended behavior? IMO the GMX_FFT_LIBRARY=fftw3 flag should be honored first and any set LD_LIBRARY_PATH ignored. Yes, but Intel decided to be compatible a.k.a. deceptive. IIRC enough people complained that it got fixed for subsequent MKL. Meanwhile, our CMake code is quite complicated enough without double-checking for every possible rare case ;-) Meanwhile, there are ways of forcing the find mechanism to find the FFTW you really want. -- Reuti *) The automatic download (like outlined in the INSTALL: -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON) of FFTW and the regression tests points to the Gromacs site, but AFAICS they were moved to box.com, hence the automatic download fails. No, the FFTW download goes to its site, and the tests download goes to gerrit.gromacs.org. None of that has changed. Mark -- 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] there are particles with all coordinates zero
Dear gmx users, I was analysing some trajectories (without any problem), and then just for testing, i used gmx check on them, and i got several warnings: Reading frame3000 time 30.000 Warning at frame 3693: there are 1 particles with all coordinates zero Reading frame4000 time 40.000 Warning at frame 4052: there are 1 particles with all coordinates zero Warning at frame 4079: there are 1 particles with all coordinates zero Warning at frame 4271: there are 1 particles with all coordinates zero Warning at frame 4519: there are 1 particles with all coordinates zero Reading frame5000 time 50.000 Warning at frame 5063: there are 1 particles with all coordinates zero Reading frame6000 time 60.000 Warning at frame 6766: there are 1 particles with all coordinates zero Reading frame7000 time 70.000 Warning at frame 7403: there are 1 particles with all coordinates zero Warning at frame 7703: there are 1 particles with all coordinates zero Reading frame8000 time 80.000 Warning at frame 8667: there are 1 particles with all coordinates zero Warning at frame 8682: there are 1 particles with all coordinates zero Reading frame9000 time 90.000 Warning at frame 9752: there are 1 particles with all coordinates zero Last frame 1 time 100.000 Are this warnings that ‘bad'? Should i run again my simulations? Again, just seeing them by VMD, and by making some analysis on them with several gromacs tools(trjconv, msd, rdf, etc) i didn’t see any problem, or get any error/warning message, so i really don’t know what could be the problem (or if there is one, i don’t know how to fix it). Hope someone can help me, Best, Carlos ps- I tried to remove pbc conditions of the system, but i’m still getting the same error: -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of Bioinformatics and Molecular Simulations. CBSM University of Talca Av. Lircay S/N, Talca, Chile T: (+56) 712201 798 E: carlos.navarr...@gmail.com or cnava...@utalca.cl -- 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.
