Re: [gmx-users] g_hbond
Hi, I think this may actually be a bug. g_hbond reports zero contacts in cases where I know there are many. Will examine this more thoroughly and file a redmine issue. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Associate Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ On 14 Jul 2014, at 13:24, mirko busato busato.mi...@yahoo.com wrote: thank you very much, I read the manual of g_mindist but seem produce in output only the number of contacts and the minimum distance . For my problem I would like to know all the atoms involved (all the contacts) within of 4 Å. so I can understand which atoms can do salt bridge interactions. Do you know a way to do this with g_mindist command? Thank you very much, Mirko On Monday, July 14, 2014 2:02 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/14/14, 7:44 AM, mirko busato wrote: Dear Users, I have one question for you. I would like to extract some information about salt bridge interactions (without using the gromacs command g_saltbr because it gave me some problems) between some atoms (charged negatively) of a type of monomer and some atoms (charged positively )of another type of monomer. So I created the two lists of atoms with g_select, and I made a file index like that: [ N_CRL ] 300 321 342 363 384 405 426 447 468 489 510 531 552 573 594 615 636 657 678 699 720 741 762 783 804 825 846 867 888 909 930 951 972 993 1014 1035 1056 1077 1098 1119 [ OX_ITA ] 168 181 194 207 220 233 246 259 272 285 and then I used g_hbond to extract the contacts of these 2 lists of atoms within 4 Å. in this way: g_hbond_d -f eq4.gro -s eq3.tpr -n index.ndx -hbn hbond.ndx -contact -r2 0.4 -r 0.4 I wouldn't use g_hbond like this; g_mindist -on is more straightforward for calculating simple contacts. I noticed a strange thing, if I change the order of the groups in the index.ndx file,like that: [ OX_ITA ] 168 181 194 207 220 233 246 259 272 285 [ N_CRL ] 300 321 342 363 384 405 426 447 468 489 510 531 552 573 594 615 636 657 678 699 720 741 762 783 804 825 846 867 888 909 930 951 972 993 1014 1035 1056 1077 1098 1119 I obtain no contacts, and it is wrong because actually I didn't change the atoms of the groups. Could you help me about it ? Order of the groups in the index file is irrelevant; it doesn't seem likely that this is the only issue. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_hbond
No. Strike that. The number of contacts is just reported the wrong way. It says Average number of contacts per timeframe 0.000… in the terminal but hbnum.xvg says different. Not sure if this applies to your problem. Erik Erik Marklund, PhD Postdoctoral Research Associate Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ On 15 Jul 2014, at 10:22, Erik Marklund erik.markl...@chem.ox.ac.uk wrote: Hi, I think this may actually be a bug. g_hbond reports zero contacts in cases where I know there are many. Will examine this more thoroughly and file a redmine issue. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Associate Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ On 14 Jul 2014, at 13:24, mirko busato busato.mi...@yahoo.com wrote: thank you very much, I read the manual of g_mindist but seem produce in output only the number of contacts and the minimum distance . For my problem I would like to know all the atoms involved (all the contacts) within of 4 Å. so I can understand which atoms can do salt bridge interactions. Do you know a way to do this with g_mindist command? Thank you very much, Mirko On Monday, July 14, 2014 2:02 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/14/14, 7:44 AM, mirko busato wrote: Dear Users, I have one question for you. I would like to extract some information about salt bridge interactions (without using the gromacs command g_saltbr because it gave me some problems) between some atoms (charged negatively) of a type of monomer and some atoms (charged positively )of another type of monomer. So I created the two lists of atoms with g_select, and I made a file index like that: [ N_CRL ] 300 321 342 363 384 405 426 447 468 489 510 531 552 573 594 615 636 657 678 699 720 741 762 783 804 825 846 867 888 909 930 951 972 993 1014 1035 1056 1077 1098 1119 [ OX_ITA ] 168 181 194 207 220 233 246 259 272 285 and then I used g_hbond to extract the contacts of these 2 lists of atoms within 4 Å. in this way: g_hbond_d -f eq4.gro -s eq3.tpr -n index.ndx -hbn hbond.ndx -contact -r2 0.4 -r 0.4 I wouldn't use g_hbond like this; g_mindist -on is more straightforward for calculating simple contacts. I noticed a strange thing, if I change the order of the groups in the index.ndx file,like that: [ OX_ITA ] 168 181 194 207 220 233 246 259 272 285 [ N_CRL ] 300 321 342 363 384 405 426 447 468 489 510 531 552 573 594 615 636 657 678 699 720 741 762 783 804 825 846 867 888 909 930 951 972 993 1014 1035 1056 1077 1098 1119 I obtain no contacts, and it is wrong because actually I didn't change the atoms of the groups. Could you help me about it ? Order of the groups in the index file is irrelevant; it doesn't seem likely that this is the only issue. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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] Error in system_inflate.gro coordinates does not match
hello everyone now i got the minimize structure after addition of water and ions (14 cl-) i have been select the genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA -nname CL -nn 14 13 th option sol in out put how can i analyze my structure means is it ok or not because next step is equilibration kindly help On Sat, Jul 12, 2014 at 2:48 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/11/14, 3:18 AM, RINU KHATTRI wrote: hello i am following the lysozyme tutorial editconf -f system_shrink20.gro -o newbox.gro -bt dodecahedron -d 1.0 Don't alter the box like this; it's totally nonsensical. solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro but after running second command i got error solvate command not found gmx solvate is also not working The tutorial corresponds to version 5.0; if you're using an older version, the command is called genbox. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How can I add subsequent simulations?
Dear all, I have each of 10 ns five simulations which were subsequently run. How can I join these simulations? Best regards, Batsaikhan -- 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 - Dimer Simulation problems
Hi, I have been running a short MD simulation (100ns) on a dimer protein. The two monomers are identical, after looking into your suggestions on http://www.gromacs.org/Documentation/How-tos/Multiple_Chains I have set up the system with waters and ions. The topol.top to look like this: ; ; File 'topol.top' was generated ; By user: michaelc (1128283773) ; On host: 104844CTHDT.local ; At date: Tue Jul 1 12:30:36 2014 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.6.5 ; ; Command line was: ; /usr/local/gromacs/bin/pdb2gmx -f BCL6_584_pseudo_apo.pdb -o BCL6_584_pseudo_apo.gro -water tip3p -ignh ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include amber99sb.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_A.itp #include topol_Protein_chain_B.itp ; Include water topology #include amber99sb.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include amber99sb.ff/ions.itp [ system ] ; Name BCL6_584_pseudo_apo in water [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 SOL 40832 NA 76 CL 79 I have then run a short minimisation and equilibration which ran successfully. I then ran a production MD run of 100ns. The md.mdp looks like this: title = Protein-ligand complex MD simulation ; Run parameters integrator = md; leap-frog integrator nsteps = 5000 ; 2 * 5000 = 10 ps (100 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 0 ; suppress .trr output nstvout = 0 ; suppress .trr output nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps nstxtcout = 1000 ; write .xtc trajectory every 2 ps energygrps = System ; Bond parameters continuation= yes ; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) rvdw= 1.4 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Water_and_ions; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; assign velocities from Maxwell distribution After this simulation finished I obtained the resultant .xtc and .tpr files. The system was then corrected to remove any problems of drifting cause by PBC and the system was centered on the protein. This was done using the following commands: trjconv -s md_0_100.tpr -f md_0_100.xtc -o protein.xtc tpbconv -s md0_100.tpr -o protein.tpr Choosing the group 1 (Protein). trjconv -s protein.tpr -f protein.xtc -o protein.gro -dump 0 Choosing the group 1 (Protein). trjconv -s protein.tpr -f protein.xtc -o protein_fit.xtc -fit rot+trans Chossing the group 4 (Backbone) and the system 1 (Protein) to write to disk. After analysing the output it appears that after around 50ns something very strange happens and my simulation see a large jump in RMSD to over 5A. This continues to happen for the last 40ns of the simulation. Upon visualisation it would appear that the dimer dissociates into two monomers. There is no real reason for this and it appears to happen randomly for the last 50 ns of the simulation. Have you come across this problem before? Do you think that I should
Re: [gmx-users] Gromacs - Dimer Simulation problems
Hi Michael, This used to happen in my simulations also. Try using nojump for your xtc file and re-plot the rmsd. I presume the jump that you see in your rmsd is a sudden jump and not a gradual one. If its a sudden jump then this will solve the problem. if you observe your simulation in ngmx you can see that at the point where rmsd jumps, one of your monomer might go outside the box. Try this and see. Good luck kavya On Tue, Jul 15, 2014 at 3:58 PM, Michael Carter michael.car...@icr.ac.uk wrote: Hi, I have been running a short MD simulation (100ns) on a dimer protein. The two monomers are identical, after looking into your suggestions on http://www.gromacs.org/Documentation/How-tos/Multiple_Chains I have set up the system with waters and ions. The topol.top to look like this: ; ; File 'topol.top' was generated ; By user: michaelc (1128283773) ; On host: 104844CTHDT.local ; At date: Tue Jul 1 12:30:36 2014 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.6.5 ; ; Command line was: ; /usr/local/gromacs/bin/pdb2gmx -f BCL6_584_pseudo_apo.pdb -o BCL6_584_pseudo_apo.gro -water tip3p -ignh ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include amber99sb.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_A.itp #include topol_Protein_chain_B.itp ; Include water topology #include amber99sb.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include amber99sb.ff/ions.itp [ system ] ; Name BCL6_584_pseudo_apo in water [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 SOL 40832 NA 76 CL 79 I have then run a short minimisation and equilibration which ran successfully. I then ran a production MD run of 100ns. The md.mdp looks like this: title = Protein-ligand complex MD simulation ; Run parameters integrator = md; leap-frog integrator nsteps = 5000 ; 2 * 5000 = 10 ps (100 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 0 ; suppress .trr output nstvout = 0 ; suppress .trr output nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps nstxtcout = 1000 ; write .xtc trajectory every 2 ps energygrps = System ; Bond parameters continuation= yes ; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) rvdw= 1.4 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Water_and_ions; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; assign velocities from Maxwell distribution After this simulation finished I obtained the resultant .xtc and .tpr files. The system was then corrected to remove any problems of drifting cause by PBC and the system was centered on the protein. This was done using the following commands: trjconv -s md_0_100.tpr -f md_0_100.xtc -o protein.xtc tpbconv -s md0_100.tpr -o protein.tpr Choosing the group 1 (Protein). trjconv -s protein.tpr -f protein.xtc -o protein.gro -dump 0 Choosing the group 1 (Protein). trjconv -s
Re: [gmx-users] Gromacs - Dimer Simulation problems
Hi Kavya, That worked perfectly. Thank you. Cheers, Michael On 15/07/2014 11:43, Kavyashree M hmkv...@gmail.com wrote: Hi Michael, This used to happen in my simulations also. Try using nojump for your xtc file and re-plot the rmsd. I presume the jump that you see in your rmsd is a sudden jump and not a gradual one. If its a sudden jump then this will solve the problem. if you observe your simulation in ngmx you can see that at the point where rmsd jumps, one of your monomer might go outside the box. Try this and see. Good luck kavya On Tue, Jul 15, 2014 at 3:58 PM, Michael Carter michael.car...@icr.ac.uk wrote: Hi, I have been running a short MD simulation (100ns) on a dimer protein. The two monomers are identical, after looking into your suggestions on http://www.gromacs.org/Documentation/How-tos/Multiple_Chains I have set up the system with waters and ions. The topol.top to look like this: ; ; File 'topol.top' was generated ; By user: michaelc (1128283773) ; On host: 104844CTHDT.local ; At date: Tue Jul 1 12:30:36 2014 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.6.5 ; ; Command line was: ; /usr/local/gromacs/bin/pdb2gmx -f BCL6_584_pseudo_apo.pdb -o BCL6_584_pseudo_apo.gro -water tip3p -ignh ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include amber99sb.ff/forcefield.itp ; Include chain topologies #include topol_Protein_chain_A.itp #include topol_Protein_chain_B.itp ; Include water topology #include amber99sb.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include amber99sb.ff/ions.itp [ system ] ; Name BCL6_584_pseudo_apo in water [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 SOL 40832 NA 76 CL 79 I have then run a short minimisation and equilibration which ran successfully. I then ran a production MD run of 100ns. The md.mdp looks like this: title = Protein-ligand complex MD simulation ; Run parameters integrator = md; leap-frog integrator nsteps = 5000 ; 2 * 5000 = 10 ps (100 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 0 ; suppress .trr output nstvout = 0 ; suppress .trr output nstenergy = 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps nstxtcout = 1000 ; write .xtc trajectory every 2 ps energygrps = System ; Bond parameters continuation= yes ; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) rvdw= 1.4 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Water_and_ions; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; assign velocities from Maxwell distribution After this simulation finished I obtained the resultant .xtc and .tpr files. The system was then corrected to remove any problems of drifting cause by PBC and the system was centered on the protein. This was done using the following commands: trjconv -s md_0_100.tpr -f md_0_100.xtc -o protein.xtc tpbconv -s md0_100.tpr -o protein.tpr Choosing the group 1
[gmx-users] .rtp file - how to define improper dihedrals?
Dear Gromacs experts, Let's say I want to keep in plane such a structure: B | A /\ C D What is the proper order of atoms for CHARMM22 force field in aminoacids.rtp file under [ impropers ] section? Is it: A C D B 0.0 200.0 ? Does the order or C B and D matter at all? Or the central A atom should be at the end? Thank you, Dawid Grabarek -- 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] CELLmicrocosmos neXt: 1st Call for Abstracts
Dear Colleagues, I would like to invite your contributions to our workshop which will celebrate the first 10 years of our CELLmicrocosmos project. It will take place at the German Conference on Bioinformatics in Bielefeld, Germany at the 28th September 2014. Especially membrane and vesicle modeling and simulation with GROMACS are a very interesting topic for us: CELLmicrocosmos neXt workshop: 1st Call for Abstracts A primary vision of Integrative Bioinformatics is the creation of a virtual cell. Cell Modeling and Visualization is an immense interdisiplinary task. For this purpose, in the context of the /German Conference of Bioinformatics (28.09. - 01.10.2014)/, the first CELLmicrocosmos neXt workshop will take place in /Bielefeld at the 28.09.2014/. During this event, 10 years of the CELLmicrocosmos project will be celebrated by presenting CELLmicrocosmos X and an additional hands-on workshop session. The submission for extended abstracts is now open! All topics related to cell visualization, modeling and simulation are welcome! These topics include e.g.: * Integrative Bioinformatics * Structural Bioinformatics * Cell Modeling and Visualization * Molecular Modeling and Visualization * Membrane and Vesicle Simulation * Network Analysis and Visualization * Data Integration * Text mining * Microscopic Image Segmentation * Biological Interactive Web Visualization * Stereoscopic 3D Visualization * Subcellular Localization More information and the complete call you will find at: http://neXt.CELLmicrocosmos.org The submission deadline is the 10th August 2014. For questions and submissions, please contact us at: n...@cellmicrocosmos.org On behalf of the program committee, Björn Sommer -- 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] more than 99,999 atoms in conf.gro
Hi
I am trying to run a simulation with more than 99,999 atoms in a conf.gro
file.
However, when I run grompp I get an error
Fatal error:
Something is wrong in the coordinate formatting of file conf.gro. Note that
gro is fixed format (see the manual)
As suggested in the online manual, I am using the following format to write
conf.gro by a Python script:
{0:5d}{1:5s}{2:5s}{3:5d}{4:8.3f}{5:8.3f}{6:8.3f}.
Could anyone please suggest me how to resolve the issue?
Thanks,
Sikandar
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Re: [gmx-users] more than 99,999 atoms in conf.gro
Hi Sikandar,
Did you try resetting your atom number to 1 as it reaches 10?
I hope this would resolve the issue.
Chandan
On Tue, Jul 15, 2014 at 3:43 PM, Sikandar Mashayak symasha...@gmail.com
wrote:
Hi
I am trying to run a simulation with more than 99,999 atoms in a conf.gro
file.
However, when I run grompp I get an error
Fatal error:
Something is wrong in the coordinate formatting of file conf.gro. Note that
gro is fixed format (see the manual)
As suggested in the online manual, I am using the following format to write
conf.gro by a Python script:
{0:5d}{1:5s}{2:5s}{3:5d}{4:8.3f}{5:8.3f}{6:8.3f}.
Could anyone please suggest me how to resolve the issue?
Thanks,
Sikandar
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Re: [gmx-users] illegal instruction while using mdrun command
Hi, I would not have thought that was possible, but the recommended solution is to compile mdrun for the machine you plan to use it on. See http://www.gromacs.org/Documentation/Installation_Instructions_4.6#4.3.1._Portability_aspects for some details. Mark On Tue, Jul 15, 2014 at 5:00 AM, Andy Chao ac...@energiaq.com wrote: Dear GROMACS Users: I used the C4mimNTf2 ionic liquid TOP and GRO files to run MD simulation. Here are the commands that I used: grompp -f em.mdp -c C4mimNTf2.gro -p c4mimNTf2.top -o NPT.tpr mdrun -v -deffnm NPT I got the following error messages: Reading file NPT.tpr Version 4.6.5 (single precision) Using 1 MPI thread Using 1 OpenMP thread Compiled acceleration: SSE4.1 (Gromacs could use AVX_256 on this machine, which is better) Illegal instruction (core dumped).. Would you please explain the reason? How to fix this problem? Thanks! Andy -- 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] Going from OPLS-AA dihedrals to CHARMM22 dihedrals.
Dear Gromacs experts, I have following issue. I need torsional parameters from this publication: D. V. Dmitrienko et al., Biochemistry (Moscow), 2006, Vol. 71, No. 10, 1133-1152 where OPLS-AA FF has been used but I need to adapt them for CHARMM22 FF. Now the thing is that there are two different torsional energy expression used in those FFs. How can I go from one to another? To be precise I want to adapt parameters from the above mentioned publication to expression for torsional potential from this publication: N. Reuter et al., J. Phys. Chem. B, 2002, Vol. 106, 6310-6321 Any help will be appreciated. Best wishes, Dawid Grabarek -- 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] more than 99,999 atoms in conf.gro
Thanks Chandan it worked!
On Tue, Jul 15, 2014 at 8:56 AM, Chandan Choudhury iitd...@gmail.com
wrote:
Hi Sikandar,
Did you try resetting your atom number to 1 as it reaches 10?
I hope this would resolve the issue.
Chandan
On Tue, Jul 15, 2014 at 3:43 PM, Sikandar Mashayak symasha...@gmail.com
wrote:
Hi
I am trying to run a simulation with more than 99,999 atoms in a conf.gro
file.
However, when I run grompp I get an error
Fatal error:
Something is wrong in the coordinate formatting of file conf.gro. Note
that
gro is fixed format (see the manual)
As suggested in the online manual, I am using the following format to
write
conf.gro by a Python script:
{0:5d}{1:5s}{2:5s}{3:5d}{4:8.3f}{5:8.3f}{6:8.3f}.
Could anyone please suggest me how to resolve the issue?
Thanks,
Sikandar
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Re: [gmx-users] limitation of no. of atoms in the .gro file
Thanks Mark. Yes, I meant to ask about the width of the atom number field. After 9, I am renumbering the atoms starting with 0 and it works now. Thanks, Sikandar On Tue, Jul 15, 2014 at 9:39 AM, Mark Abraham mark.j.abra...@gmail.com wrote: No, but there is a limit on the width of the atom-number field. Is that the question you meant to ask? :-) In practice, in making such a file, you should wrap from 99 or whatever to 0, because GROMACS only ever checks to see that the value changes. Mark On Mon, Jul 14, 2014 at 10:13 PM, Sikandar Mashayak symasha...@gmail.com wrote: Hi Is there a limitation on number of atoms in .gro file? Thanks, Sikandar -- 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. -- 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] GPU build error
Hi, I am trying to build with GPU acceleration, and I get the following build error. However, if set GMX_GPU=OFF and keep MPI=ON it compiles. Could anyone please suggest how to resolve the issue? Thanks, Sikandar /home/projects/cuda/6.0.37/bin/nvcc /home/smashay/gromacs/gromacs-5.0/src/gromacs/mdlib/nbnxn_cuda/ nbnxn_cuda_data_mgmt.cu -c -o /home/smashay/gromacs/build/src/gromacs/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir//./nbnxn_cuda_generated_nbnxn_cuda_data_mgmt.cu.o -ccbin /home/projects/intel/compilers/2013/13.SP1.1.106/bin/icc -m64 -DHAVE_CONFIG_H -DBOOST_NO_TYPEID -Xcompiler ,\-mavx\,\-w3\,\-wd111\,\-wd177\,\-wd181\,\-wd193\,\-wd271\,\-wd304\,\-wd383\,\-wd424\,\-wd444\,\-wd522\,\-wd593\,\-wd869\,\-wd981\,\-wd1418\,\-wd1419\,\-wd1572\,\-wd1599\,\-wd2259\,\-wd2415\,\-wd2547\,\-wd2557\,\-wd3280\,\-wd3346\,\-wd1782\,\-ip\,\-funroll-all-loops\,\-alias-const\,\-ansi-alias\,\-O3\,\-DNDEBUG\ -gencode arch=compute_20,code=sm_20 -gencode arch=compute_20,code=sm_21 -gencode arch=compute_30,code=sm_30 -gencode arch=compute_35,code=sm_35 -gencode arch=compute_35,code=compute_35 -use_fast_math -DNVCC -I/home/smashay/gromacs/gromacs-5.0/src/gromacs/mdlib/nbnxn_cuda -I/home/projects/cuda/6.0.37/include -I/home/smashay/gromacs/gromacs-5.0/src -I/home/smashay/gromacs/gromacs-5.0/src/external/thread_mpi/include -I/home/smashay/gromacs/build/src -I/home/smashay/gromacs/build/src/gromacs/utility -I/home/smashay/gromacs/gromacs-5.0/src/gromacs/legacyheaders -I/home/smashay/gromacs/include -I/home/smashay/gromacs/gromacs-5.0/src/external/boost -I/home/smashay/gromacs/gromacs-5.0/src/external/tng_io/include -I/home/smashay/gromacs/build/src/external/tng_io/include -I/home/projects/cuda/6.0.37/include In file included from /home/smashay/gromacs/gromacs-5.0/src/external/boost/boost/config.hpp(35), from /home/smashay/gromacs/gromacs-5.0/src/external/boost/boost/smart_ptr/scoped_ptr.hpp(14), from /home/smashay/gromacs/gromacs-5.0/src/external/boost/boost/scoped_ptr.hpp(14), from /home/smashay/gromacs/gromacs-5.0/src/gromacs/utility/common.h(50), from /home/smashay/gromacs/gromacs-5.0/src/gromacs/mdlib/nbnxn_cuda/ nbnxn_cuda_data_mgmt.cu(63): /home/smashay/gromacs/gromacs-5.0/src/external/boost/boost/config/compiler/intel.hpp(40): warning #47: incompatible redefinition of macro BOOST_COMPILER (declared at line 11 of /home/smashay/gromacs/gromacs-5.0/src/external/boost/boost/config/compiler/nvcc.hpp) #define BOOST_COMPILER Intel C++ version BOOST_STRINGIZE(BOOST_INTEL_CXX_VERSION) ^ /home/smashay/gromacs/gromacs-5.0/src/external/boost/boost/config/suffix.hpp(496): error: identifier __int128 is undefined /home/smashay/gromacs/gromacs-5.0/src/external/boost/boost/config/suffix.hpp(497): error: expected a ; -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem related to solvating CNT and then removing out the molecules inside CNT
Hey Justin, I think I understood the problem. When I removed the solvent from inside CNT, I kept the numbering of atoms just like before without actually making a new strictly increasing order numbering. But now when I see that after the energy minimization the new pdb file got arranged strictly by increasing order. As an example. After deleting atoms inside the CNT, my .gro file did not had the atom no 6292, but after energy minimisation the em.gro file contains the atom no 6292. This must have created a renumbering of the atoms. Not good I suppose. Please suggest what to do? The concern is that whether to renumber the molecules after removing the water from inside the CNT or not? Thanking You, Vivek Sinha On Tue, Jul 15, 2014 at 9:14 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/14/14, 9:38 AM, vivek sinha wrote: Hi Justin, I dont have the periodic molecules so do I include anything in the .mdp file? Also when I grompp this I get no warning or error or note. But when I mdrun it, I get WARNING: Listed nonbonded interaction between particles 35 and 114 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. and then the program terminates after displaying a segmentation fault error. Please provide any valuable suggestions. Your system is blowing up. It's a hard situation to diagnose with limited information, but something is almost certainly wrong with your topology. http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_ Unstable_System -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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] GPU build error
Hi, Never seen this error, it looks like the compiler chokes on some boost header. At the same time, the __int128-related error seems to indicate that setting the -gcc-version=XYZ flag to some older gcc (e.g. 4.5/4.6) and by that requesting compatibility mode with the specified gcc version could solve he latter error. However, note that: - CUDA typically supports a single Intel compiler version, based on the include/host_config.h line 70 for CUDA 6.0 this seems to te be v13.10 - whatever that is equivalent with in 2013 SP notation; - You will typically get better performance with a modern gcc, e.g. 4.8, than with icc. Cheers, -- Szilárd On Tue, Jul 15, 2014 at 7:35 PM, Sikandar Mashayak symasha...@gmail.com wrote: Hi, I am trying to build with GPU acceleration, and I get the following build error. However, if set GMX_GPU=OFF and keep MPI=ON it compiles. Could anyone please suggest how to resolve the issue? Thanks, Sikandar /home/projects/cuda/6.0.37/bin/nvcc /home/smashay/gromacs/gromacs-5.0/src/gromacs/mdlib/nbnxn_cuda/ nbnxn_cuda_data_mgmt.cu -c -o /home/smashay/gromacs/build/src/gromacs/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir//./nbnxn_cuda_generated_nbnxn_cuda_data_mgmt.cu.o -ccbin /home/projects/intel/compilers/2013/13.SP1.1.106/bin/icc -m64 -DHAVE_CONFIG_H -DBOOST_NO_TYPEID -Xcompiler ,\-mavx\,\-w3\,\-wd111\,\-wd177\,\-wd181\,\-wd193\,\-wd271\,\-wd304\,\-wd383\,\-wd424\,\-wd444\,\-wd522\,\-wd593\,\-wd869\,\-wd981\,\-wd1418\,\-wd1419\,\-wd1572\,\-wd1599\,\-wd2259\,\-wd2415\,\-wd2547\,\-wd2557\,\-wd3280\,\-wd3346\,\-wd1782\,\-ip\,\-funroll-all-loops\,\-alias-const\,\-ansi-alias\,\-O3\,\-DNDEBUG\ -gencode arch=compute_20,code=sm_20 -gencode arch=compute_20,code=sm_21 -gencode arch=compute_30,code=sm_30 -gencode arch=compute_35,code=sm_35 -gencode arch=compute_35,code=compute_35 -use_fast_math -DNVCC -I/home/smashay/gromacs/gromacs-5.0/src/gromacs/mdlib/nbnxn_cuda -I/home/projects/cuda/6.0.37/include -I/home/smashay/gromacs/gromacs-5.0/src -I/home/smashay/gromacs/gromacs-5.0/src/external/thread_mpi/include -I/home/smashay/gromacs/build/src -I/home/smashay/gromacs/build/src/gromacs/utility -I/home/smashay/gromacs/gromacs-5.0/src/gromacs/legacyheaders -I/home/smashay/gromacs/include -I/home/smashay/gromacs/gromacs-5.0/src/external/boost -I/home/smashay/gromacs/gromacs-5.0/src/external/tng_io/include -I/home/smashay/gromacs/build/src/external/tng_io/include -I/home/projects/cuda/6.0.37/include In file included from /home/smashay/gromacs/gromacs-5.0/src/external/boost/boost/config.hpp(35), from /home/smashay/gromacs/gromacs-5.0/src/external/boost/boost/smart_ptr/scoped_ptr.hpp(14), from /home/smashay/gromacs/gromacs-5.0/src/external/boost/boost/scoped_ptr.hpp(14), from /home/smashay/gromacs/gromacs-5.0/src/gromacs/utility/common.h(50), from /home/smashay/gromacs/gromacs-5.0/src/gromacs/mdlib/nbnxn_cuda/ nbnxn_cuda_data_mgmt.cu(63): /home/smashay/gromacs/gromacs-5.0/src/external/boost/boost/config/compiler/intel.hpp(40): warning #47: incompatible redefinition of macro BOOST_COMPILER (declared at line 11 of /home/smashay/gromacs/gromacs-5.0/src/external/boost/boost/config/compiler/nvcc.hpp) #define BOOST_COMPILER Intel C++ version BOOST_STRINGIZE(BOOST_INTEL_CXX_VERSION) ^ /home/smashay/gromacs/gromacs-5.0/src/external/boost/boost/config/suffix.hpp(496): error: identifier __int128 is undefined /home/smashay/gromacs/gromacs-5.0/src/external/boost/boost/config/suffix.hpp(497): error: expected a ; -- 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] illegal instruction while using mdrun command
On Tue, Jul 15, 2014 at 5:41 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, I would not have thought that was possible, It can happen e.g. if you configure with SSE4.1 acceleration, but you also use e.g. the -mfma4 or -march=bdver1 compiler flag. but the recommended solution is to compile mdrun for the machine you plan to use it on. See http://www.gromacs.org/Documentation/Installation_Instructions_4.6#4.3.1._Portability_aspects for some details. Mark On Tue, Jul 15, 2014 at 5:00 AM, Andy Chao ac...@energiaq.com wrote: Dear GROMACS Users: I used the C4mimNTf2 ionic liquid TOP and GRO files to run MD simulation. Here are the commands that I used: grompp -f em.mdp -c C4mimNTf2.gro -p c4mimNTf2.top -o NPT.tpr mdrun -v -deffnm NPT I got the following error messages: Reading file NPT.tpr Version 4.6.5 (single precision) Using 1 MPI thread Using 1 OpenMP thread Compiled acceleration: SSE4.1 (Gromacs could use AVX_256 on this machine, which is better) Illegal instruction (core dumped).. Would you please explain the reason? How to fix this problem? Thanks! Andy -- 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. -- 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] illegal instruction while using mdrun command
So, Andy, could you share the log file the above command produced? -- Szilárd On Tue, Jul 15, 2014 at 11:22 PM, Szilárd Páll pall.szil...@gmail.com wrote: On Tue, Jul 15, 2014 at 5:41 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, I would not have thought that was possible, It can happen e.g. if you configure with SSE4.1 acceleration, but you also use e.g. the -mfma4 or -march=bdver1 compiler flag. but the recommended solution is to compile mdrun for the machine you plan to use it on. See http://www.gromacs.org/Documentation/Installation_Instructions_4.6#4.3.1._Portability_aspects for some details. Mark On Tue, Jul 15, 2014 at 5:00 AM, Andy Chao ac...@energiaq.com wrote: Dear GROMACS Users: I used the C4mimNTf2 ionic liquid TOP and GRO files to run MD simulation. Here are the commands that I used: grompp -f em.mdp -c C4mimNTf2.gro -p c4mimNTf2.top -o NPT.tpr mdrun -v -deffnm NPT I got the following error messages: Reading file NPT.tpr Version 4.6.5 (single precision) Using 1 MPI thread Using 1 OpenMP thread Compiled acceleration: SSE4.1 (Gromacs could use AVX_256 on this machine, which is better) Illegal instruction (core dumped).. Would you please explain the reason? How to fix this problem? Thanks! Andy -- 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. -- 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 can I add subsequent simulations?
Version =4 trjcat Version =5 gmx trjcat Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -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 Batdorj Batsaikhan Sent: Tuesday, 15 July 2014 8:12 PM To: Discussion List for GROMACS Users Subject: [gmx-users] How can I add subsequent simulations? Dear all, I have each of 10 ns five simulations which were subsequently run. How can I join these simulations? Best regards, Batsaikhan -- 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] .rtp file - how to define improper dihedrals?
On 7/15/14, 8:57 AM, Dawid das wrote: Dear Gromacs experts, Let's say I want to keep in plane such a structure: B | A /\ C D What is the proper order of atoms for CHARMM22 force field in aminoacids.rtp file under [ impropers ] section? Is it: A C D B 0.0 200.0 ? Does the order or C B and D matter at all? Or the central A atom should be at the end? The central atom is listed first. The order of the remaining three atoms should be irrelevant. You can easily verify with single-point energy calculations. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Going from OPLS-AA dihedrals to CHARMM22 dihedrals.
On 7/15/14, 1:29 PM, Dawid das wrote: Dear Gromacs experts, I have following issue. I need torsional parameters from this publication: D. V. Dmitrienko et al., Biochemistry (Moscow), 2006, Vol. 71, No. 10, 1133-1152 where OPLS-AA FF has been used but I need to adapt them for CHARMM22 FF. Now the thing is that there are two different torsional energy expression used in those FFs. How can I go from one to another? To be precise I want to adapt parameters from the above mentioned publication to expression for torsional potential from this publication: N. Reuter et al., J. Phys. Chem. B, 2002, Vol. 106, 6310-6321 Any help will be appreciated. It's not wise to try to hack parameters developed for one force field into another. Dihedrals are especially dangerous, because their validity is also dependent upon the nonbonded interactions of atoms 1 and 4 in the interaction; differences in charges and LJ parameters between OPLS-AA and CHARMM will make the dihedral non-transferable. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem related to solvating CNT and then removing out the molecules inside CNT
On 7/15/14, 2:19 PM, vivek sinha wrote: Hey Justin, I think I understood the problem. When I removed the solvent from inside CNT, I kept the numbering of atoms just like before without actually making a new strictly increasing order numbering. But now when I see that after the energy minimization the new pdb file got arranged strictly by increasing order. As an example. After deleting atoms inside the CNT, my .gro file did not had the atom no 6292, but after energy minimisation the em.gro file contains the atom no 6292. This must have created a renumbering of the atoms. Not good I suppose. Please suggest what to do? The concern is that whether to renumber the molecules after removing the water from inside the CNT or not? The numbering in the input coordinate file is irrelevant. The output of mdrun is always numbered consecutively from 1. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] my log file to the mdrun error message that on Tue 15, July...
Dear GROMACS Users: Here is my log file.. Please let me know how to fix this problem. Thanks! Andy Log file opened on Tue Jul 15 21:01:52 2014 Host: server-Virtual-Machine pid: 10019 nodeid: 0 nnodes: 1 Gromacs version:VERSION 4.6.5 Precision: single Memory model: 32 bit MPI library:thread_mpi OpenMP support: enabled GPU support:disabled invsqrt routine:gmx_software_invsqrt(x) CPU acceleration: SSE4.1 FFT library:fftw-3.3.3-sse2-avx Large file support: enabled RDTSCP usage: enabled Built on: Sun Dec 15 03:59:22 UTC 2013 Built by: buildd@roseapple [CMAKE] Build OS/arch: Linux 3.2.0-37-generic i686 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Xeon(R) CPU E5530 @ 2.40GHz Build CPU family: 6 Model: 26 Stepping: 5 Build CPU features: apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 C compiler: /usr/bin/i686-linux-gnu-gcc GNU gcc-4.8.real (Ubuntu/Linaro 4.8.2-10ubuntu1) 4.8.2 C compiler flags: -msse4.1-Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused -Wunused-value -Wno-unused-parameter -Wno-array-bounds -Wno-maybe-uninitialized -Wno-strict-overflow -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -O3 -DNDEBUG :-) G R O M A C S (-: Gromacs Runs On Most of All Computer Systems :-) VERSION 4.6.5 (-: Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2012,2013, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. :-) mdrun (-: PLEASE READ AND CITE THE FOLLOWING REFERENCE B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 (2008) pp. 435-447 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen GROMACS: Fast, Flexible and Free J. Comp. Chem. 26 (2005) pp. 1701-1719 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE E. Lindahl and B. Hess and D. van der Spoel GROMACS 3.0: A package for molecular simulation and trajectory analysis J. Mol. Mod. 7 (2001) pp. 306-317 --- Thank You --- PLEASE READ AND CITE THE FOLLOWING REFERENCE H. J. C. Berendsen, D. van der Spoel and R. van Drunen GROMACS: A message-passing parallel molecular dynamics implementation Comp. Phys. Comm. 91 (1995) pp. 43-56 --- Thank You --- Changing rlist from 1.05 to 1 for non-bonded 4x4 atom kernels Input Parameters: integrator = steep nsteps = 200 init-step= 0 cutoff-scheme= Verlet ns_type = Grid nstlist = 10 ndelta = 2 nstcomm = 100 comm-mode= Linear nstlog = 1000 nstxout = 0 nstvout = 0 nstfout = 0 nstcalcenergy= 100 nstenergy= 1000 nstxtcout= 0 init-t = 0 delta-t = 0.001 xtcprec = 1000 fourierspacing = 0.12 nkx = 48 nky = 48 nkz = 48 pme-order= 4 ewald-rtol = 1e-05 ewald-geometry = 0 epsilon-surface = 0 optimize-fft = FALSE ePBC = xyz bPeriodicMols= FALSE bContinuation= FALSE bShakeSOR= FALSE etc = No bPrintNHChains = FALSE nsttcouple = -1 epc = No epctype = Isotropic nstpcouple = -1 tau-p
Re: [gmx-users] Graphene topology file
Dear Justin, Thanks so much for your help. I am still unable to solve the problem of blowing up of the box. Once I am able to do correct simulation I will update here. Regards Sukriti Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University N1.3-B4-14, 50 Nanyang Avenue, Singapore 639798 Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Saturday, July 12, 2014 5:17 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file On 7/11/14, 5:42 AM, #SUKRITI GUPTA# wrote: Hi Justin, Thanks for the reply. I changed define= -dflexible to -dposres_water and removed freeze graphene group in my .mdp file and ran the energy minimization and npt again. This time for pbc= xyz, the water doesn't fly away but the graphene sheet curves and does not remain in xy plane. Is it ok for the sheet to bend during simulation and will it not effect the pbc? Applying pressure along the plane of the sheet can cause deformation. Whether or not this is physically relevant, I have no idea. Also for pbc=xy, the same problem persists as the previous one i.e. following error occurs: Step 20: The charge group starting at atom 796 moved than the distance allowed by the domain decomposition in direction X distance out of cell -0.290927 New coordinates:2.4112.0060.982 Old cell boundaries in direction X:0.0002.702 New cell boundaries in direction X:0.0002.702 --- Program mdrun, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/mdlib/domdec.c, line: 4124 Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors. Can you please suggest what can be causing the error to occur? That's a generic error suggesting the system is blowing up. http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System I know nothing about using walls, so that's the best I can suggest. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] mdrun error messages
Dear GROMACS Users:
As I mentioned, I got the following log file when I used the mdrun
command. I installed GROMACS on my virtual machine. Is there any solution
to this problem?
Thanks!
Andy
PLEASE READ AND CITE THE FOLLOWING REFERENCE
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
--- Thank You ---
Changing rlist from 1.05 to 1 for non-bonded 4x4 atom kernels
Input Parameters:
integrator = steep
nsteps = 200
init-step= 0
cutoff-scheme= Verlet
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 100
comm-mode= Linear
nstlog = 1000
nstxout = 0
nstvout = 0
nstfout = 0
nstcalcenergy= 100
nstenergy= 1000
nstxtcout= 0
init-t = 0
delta-t = 0.001
xtcprec = 1000
fourierspacing = 0.12
nkx = 48
nky = 48
nkz = 48
pme-order= 4
ewald-rtol = 1e-05
ewald-geometry = 0
epsilon-surface = 0
optimize-fft = FALSE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= FALSE
bShakeSOR= FALSE
etc = No
bPrintNHChains = FALSE
nsttcouple = -1
epc = No
epctype = Isotropic
nstpcouple = -1
tau-p= 1
ref-p (3x3):
ref-p[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref-p[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
ref-p[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress (3x3):
compress[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
compress[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
refcoord-scaling = No
posres-com (3):
posres-com[0]= 0.0e+00
posres-com[1]= 0.0e+00
posres-com[2]= 0.0e+00
posres-comB (3):
posres-comB[0]= 0.0e+00
posres-comB[1]= 0.0e+00
posres-comB[2]= 0.0e+00
verlet-buffer-drift = 0.005
rlist= 1
rlistlong= 1
nstcalclr= 10
rtpi = 0.05
coulombtype = PME
coulomb-modifier = Potential-shift
rcoulomb-switch = 0
rcoulomb = 1
vdwtype = Cut-off
vdw-modifier = Potential-shift
rvdw-switch = 0
rvdw = 1
epsilon-r= 1
epsilon-rf = inf
tabext = 1
implicit-solvent = No
gb-algorithm = Still
gb-epsilon-solvent = 80
nstgbradii = 1
rgbradii = 1
gb-saltconc = 0
gb-obc-alpha = 1
gb-obc-beta = 0.8
gb-obc-gamma = 4.85
gb-dielectric-offset = 0.009
sa-algorithm = Ace-approximation
sa-surface-tension = 2.05016
DispCorr = No
bSimTemp = FALSE
free-energy = no
nwall= 0
wall-type= 9-3
wall-atomtype[0] = -1
wall-atomtype[1] = -1
wall-density[0] = 0
wall-density[1] = 0
wall-ewald-zfac = 3
pull = no
rotation = FALSE
disre= No
disre-weighting = Conservative
disre-mixed = FALSE
dr-fc= 1000
dr-tau = 0
nstdisreout = 100
orires-fc= 0
orires-tau = 0
nstorireout = 100
dihre-fc = 0
em-stepsize = 0.01
em-tol = 10
niter= 20
fc-stepsize = 0
nstcgsteep = 1000
nbfgscorr= 10
ConstAlg = Lincs
shake-tol= 0.0001
lincs-order = 4
lincs-warnangle = 30
lincs-iter = 1
bd-fric = 0
ld-seed = 1993
cos-accel= 0
deform (3x3):
deform[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
deform[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
adress = FALSE
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1= 0
userreal2= 0
userreal3= 0
userreal4= 0
grpopts:
nrdf: 22677
ref-t: 0
tau-t: 0
anneal: No
ann-npoints: 0
acc: 0 0 0
nfreeze: N
Re: [gmx-users] Problem related to solvating CNT and then removing out the molecules inside CNT
But mdrun doesnt update these information/new numbering in the topology file. I mean the topology fie would be saying that there is a bond between 101 and 105 and if I removed those atoms, the mdrun would have assignmed 101 and 105 to some other atom and hence it can create problems. Is this possible? On Wed, Jul 16, 2014 at 9:35 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/15/14, 2:19 PM, vivek sinha wrote: Hey Justin, I think I understood the problem. When I removed the solvent from inside CNT, I kept the numbering of atoms just like before without actually making a new strictly increasing order numbering. But now when I see that after the energy minimization the new pdb file got arranged strictly by increasing order. As an example. After deleting atoms inside the CNT, my .gro file did not had the atom no 6292, but after energy minimisation the em.gro file contains the atom no 6292. This must have created a renumbering of the atoms. Not good I suppose. Please suggest what to do? The concern is that whether to renumber the molecules after removing the water from inside the CNT or not? The numbering in the input coordinate file is irrelevant. The output of mdrun is always numbered consecutively from 1. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Error in system_inflate.gro coordinates does not match
hello every one i am working on complex with popc membrane after visualization of minimize structure (after solvation and addition of ions 14 cl-) in VMD i saw protein is moving out em.gro from the lipid membrane i dont know how to resolve it help On Tue, Jul 15, 2014 at 3:42 PM, RINU KHATTRI nickname.mi...@gmail.com wrote: hello everyone now i got the minimize structure after addition of water and ions (14 cl-) i have been select the genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA -nname CL -nn 14 13 th option sol in out put how can i analyze my structure means is it ok or not because next step is equilibration kindly help On Sat, Jul 12, 2014 at 2:48 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/11/14, 3:18 AM, RINU KHATTRI wrote: hello i am following the lysozyme tutorial editconf -f system_shrink20.gro -o newbox.gro -bt dodecahedron -d 1.0 Don't alter the box like this; it's totally nonsensical. solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro but after running second command i got error solvate command not found gmx solvate is also not working The tutorial corresponds to version 5.0; if you're using an older version, the command is called genbox. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem related to solvating CNT and then removing out the molecules inside CNT
Hey Justin, I will tell you the steps that I took for the simulation from the beginning. 1. Generated a tube online http://turin.nss.udel.edu/research/tubegenonline.html 2. Attched Hydrogen to it using pymol and converted to .gro and then .top file 3. Solvated using genbox -cp cnt_sl.gro -cs spc216.gro -o cnt_solvated.gro -p topol.top 4. Remove atoms from center using c++ script which does not numbers the atoms again. My 12663 atoms changed to 12183 after this. 5. Energy minimisation: grompp -f minim.mdp -c ___.gro -p ___.top -o em.tpr mdrun -v -deffnm em The next step about equibilating is giving a segmentation fault. The minim.mdp is --- ; minim.mdp - used as input into grompp to generate em.tpr integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist= 1; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type= grid; Method to determine neighbor list (simple, grid) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 0.9; Short-range electrostatic cut-off rvdw= 0.9; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions (yes/no) --- And I have already sent you the nvt.mdp settings that I am using. Please help me in completing my simulation. Thanking You, Vivek Sinha On Wed, Jul 16, 2014 at 1:25 PM, vivek sinha viveksinha20...@gmail.com wrote: But mdrun doesnt update these information/new numbering in the topology file. I mean the topology fie would be saying that there is a bond between 101 and 105 and if I removed those atoms, the mdrun would have assignmed 101 and 105 to some other atom and hence it can create problems. Is this possible? On Wed, Jul 16, 2014 at 9:35 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/15/14, 2:19 PM, vivek sinha wrote: Hey Justin, I think I understood the problem. When I removed the solvent from inside CNT, I kept the numbering of atoms just like before without actually making a new strictly increasing order numbering. But now when I see that after the energy minimization the new pdb file got arranged strictly by increasing order. As an example. After deleting atoms inside the CNT, my .gro file did not had the atom no 6292, but after energy minimisation the em.gro file contains the atom no 6292. This must have created a renumbering of the atoms. Not good I suppose. Please suggest what to do? The concern is that whether to renumber the molecules after removing the water from inside the CNT or not? The numbering in the input coordinate file is irrelevant. The output of mdrun is always numbered consecutively from 1. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem related to solvating CNT and then removing out the molecules inside CNT
No idea if the numbering is an issue (doubt it), but if you want to get the atoms renumbered sequentially within a coordinate file, just pass it through editconf without any manipulations. It will renumber things for you. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -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 vivek sinha Sent: Wednesday, 16 July 2014 2:53 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Problem related to solvating CNT and then removing out the molecules inside CNT Hey Justin, I will tell you the steps that I took for the simulation from the beginning. 1. Generated a tube online http://turin.nss.udel.edu/research/tubegenonline.html 2. Attched Hydrogen to it using pymol and converted to .gro and then .top file 3. Solvated using genbox -cp cnt_sl.gro -cs spc216.gro -o cnt_solvated.gro -p topol.top 4. Remove atoms from center using c++ script which does not numbers the atoms again. My 12663 atoms changed to 12183 after this. 5. Energy minimisation: grompp -f minim.mdp -c ___.gro -p ___.top -o em.tpr mdrun -v -deffnm em The next step about equibilating is giving a segmentation fault. The minim.mdp is --- ; minim.mdp - used as input into grompp to generate em.tpr integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist= 1; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type= grid; Method to determine neighbor list (simple, grid) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 0.9; Short-range electrostatic cut-off rvdw= 0.9; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions (yes/no) --- And I have already sent you the nvt.mdp settings that I am using. Please help me in completing my simulation. Thanking You, Vivek Sinha On Wed, Jul 16, 2014 at 1:25 PM, vivek sinha viveksinha20...@gmail.com wrote: But mdrun doesnt update these information/new numbering in the topology file. I mean the topology fie would be saying that there is a bond between 101 and 105 and if I removed those atoms, the mdrun would have assignmed 101 and 105 to some other atom and hence it can create problems. Is this possible? On Wed, Jul 16, 2014 at 9:35 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/15/14, 2:19 PM, vivek sinha wrote: Hey Justin, I think I understood the problem. When I removed the solvent from inside CNT, I kept the numbering of atoms just like before without actually making a new strictly increasing order numbering. But now when I see that after the energy minimization the new pdb file got arranged strictly by increasing order. As an example. After deleting atoms inside the CNT, my .gro file did not had the atom no 6292, but after energy minimisation the em.gro file contains the atom no 6292. This must have created a renumbering of the atoms. Not good I suppose. Please suggest what to do? The concern is that whether to renumber the molecules after removing the water from inside the CNT or not? The numbering in the input coordinate file is irrelevant. The output of mdrun is always numbered consecutively from 1. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to
Re: [gmx-users] Problem related to solvating CNT and then removing out the molecules inside CNT
But not renumbered in the topology file. That would be an issue then. On Wed, Jul 16, 2014 at 2:01 PM, Dallas Warren dallas.war...@monash.edu wrote: No idea if the numbering is an issue (doubt it), but if you want to get the atoms renumbered sequentially within a coordinate file, just pass it through editconf without any manipulations. It will renumber things for you. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -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 vivek sinha Sent: Wednesday, 16 July 2014 2:53 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Problem related to solvating CNT and then removing out the molecules inside CNT Hey Justin, I will tell you the steps that I took for the simulation from the beginning. 1. Generated a tube online http://turin.nss.udel.edu/research/tubegenonline.html 2. Attched Hydrogen to it using pymol and converted to .gro and then .top file 3. Solvated using genbox -cp cnt_sl.gro -cs spc216.gro -o cnt_solvated.gro -p topol.top 4. Remove atoms from center using c++ script which does not numbers the atoms again. My 12663 atoms changed to 12183 after this. 5. Energy minimisation: grompp -f minim.mdp -c ___.gro -p ___.top -o em.tpr mdrun -v -deffnm em The next step about equibilating is giving a segmentation fault. The minim.mdp is --- ; minim.mdp - used as input into grompp to generate em.tpr integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist= 1; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type= grid; Method to determine neighbor list (simple, grid) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 0.9; Short-range electrostatic cut-off rvdw= 0.9; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions (yes/no) --- And I have already sent you the nvt.mdp settings that I am using. Please help me in completing my simulation. Thanking You, Vivek Sinha On Wed, Jul 16, 2014 at 1:25 PM, vivek sinha viveksinha20...@gmail.com wrote: But mdrun doesnt update these information/new numbering in the topology file. I mean the topology fie would be saying that there is a bond between 101 and 105 and if I removed those atoms, the mdrun would have assignmed 101 and 105 to some other atom and hence it can create problems. Is this possible? On Wed, Jul 16, 2014 at 9:35 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/15/14, 2:19 PM, vivek sinha wrote: Hey Justin, I think I understood the problem. When I removed the solvent from inside CNT, I kept the numbering of atoms just like before without actually making a new strictly increasing order numbering. But now when I see that after the energy minimization the new pdb file got arranged strictly by increasing order. As an example. After deleting atoms inside the CNT, my .gro file did not had the atom no 6292, but after energy minimisation the em.gro file contains the atom no 6292. This must have created a renumbering of the atoms. Not good I suppose. Please suggest what to do? The concern is that whether to renumber the molecules after removing the water from inside the CNT or not? The numbering in the input coordinate file is irrelevant. The output of mdrun is always numbered consecutively from 1. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at
Re: [gmx-users] Simulation at high temperature
Hi, I first simulated my protein system at 300 K. Now I want to simulate the same protein system at high temperature (353.15 K). So, do I need to perform the npt and nvt equilibration again at 353.1 K first and then the final production run ?? Will it be okay to change the temp only in the production run file alone and continue the simulation ? Please respond Regards --- Bharat -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem related to solvating CNT and then removing out the molecules inside CNT
You are just removing waters, so unless it is mixed up with the tube (which it shouldn't be), then the topology doesn't care. All it really cares about is the atom names and the order. Your topology should be something like (the .itp could be included within the .top): CNT.itp will contain [ moleculetype ] CNT [ atoms ] [ bonds ] ... Etc topol.top will contain #include CNT.itp #include correct water model.itp [ system ] CNT with water outside only [molecules ] CNT1 SOLsome large number conf.gro will contain CNT with water outside only somelargenumber 1CNT C1 1 x y z some#SOL OW some# x y z some#SOL HW1 etc As long as the order in the topology and the coordinate file matches all will work. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -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 vivek sinha Sent: Wednesday, 16 July 2014 3:15 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Problem related to solvating CNT and then removing out the molecules inside CNT But not renumbered in the topology file. That would be an issue then. On Wed, Jul 16, 2014 at 2:01 PM, Dallas Warren dallas.war...@monash.edu wrote: No idea if the numbering is an issue (doubt it), but if you want to get the atoms renumbered sequentially within a coordinate file, just pass it through editconf without any manipulations. It will renumber things for you. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -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 vivek sinha Sent: Wednesday, 16 July 2014 2:53 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Problem related to solvating CNT and then removing out the molecules inside CNT Hey Justin, I will tell you the steps that I took for the simulation from the beginning. 1. Generated a tube online http://turin.nss.udel.edu/research/tubegenonline.html 2. Attched Hydrogen to it using pymol and converted to .gro and then .top file 3. Solvated using genbox -cp cnt_sl.gro -cs spc216.gro -o cnt_solvated.gro -p topol.top 4. Remove atoms from center using c++ script which does not numbers the atoms again. My 12663 atoms changed to 12183 after this. 5. Energy minimisation: grompp -f minim.mdp -c ___.gro -p ___.top - o em.tpr mdrun -v -deffnm em The next step about equibilating is giving a segmentation fault. The minim.mdp is --- ; minim.mdp - used as input into grompp to generate em.tpr integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist= 1; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type= grid; Method to determine neighbor list (simple, grid) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 0.9; Short-range electrostatic cut-off rvdw= 0.9; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions (yes/no) --- And I have already sent you the nvt.mdp settings that I am using. Please help me in completing my simulation. Thanking You, Vivek Sinha On Wed, Jul 16, 2014 at 1:25 PM, vivek sinha viveksinha20...@gmail.com wrote: But mdrun doesnt update these information/new numbering in the topology file. I mean the topology fie would be saying that there is a bond between 101 and 105 and if I removed those atoms, the mdrun would have assignmed 101 and 105 to some other atom and hence it can create problems. Is this possible? On Wed, Jul 16, 2014 at 9:35 AM, Justin Lemkul
Re: [gmx-users] Error in system_inflate.gro coordinates does not match
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Switch on periodic image in VMD and you will that it is not a problem at all. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -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 RINU KHATTRI Sent: Wednesday, 16 July 2014 3:24 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Error in system_inflate.gro coordinates does not match hello gromacs users i saw in vmd system.gro its little bit ok very small fragment of protein is out but in shrinkage.gro file box and protein is separated ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include strong_posre.itp #endif ; Include ligand topology #include drag.itp ; Include POPC chain topology #include popc.itp ; Include water topology #include gromos53a6_lipid.ff/spc.itp my topology file kindly help thanks in advance On Wed, Jul 16, 2014 at 10:20 AM, RINU KHATTRI nickname.mi...@gmail.com wrote: hello every one i am working on complex with popc membrane after visualization of minimize structure (after solvation and addition of ions 14 cl-) in VMD i saw protein is moving out em.gro from the lipid membrane i dont know how to resolve it help On Tue, Jul 15, 2014 at 3:42 PM, RINU KHATTRI nickname.mi...@gmail.com wrote: hello everyone now i got the minimize structure after addition of water and ions (14 cl-) i have been select the genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA - nname CL -nn 14 13 th option sol in out put how can i analyze my structure means is it ok or not because next step is equilibration kindly help On Sat, Jul 12, 2014 at 2:48 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/11/14, 3:18 AM, RINU KHATTRI wrote: hello i am following the lysozyme tutorial editconf -f system_shrink20.gro -o newbox.gro -bt dodecahedron -d 1.0 Don't alter the box like this; it's totally nonsensical. solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro but after running second command i got error solvate command not found gmx solvate is also not working The tutorial corresponds to version 5.0; if you're using an older version, the command is called genbox. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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] Error in system_inflate.gro coordinates does not match
hello every one i saw it in vmd representation -periodic but still protein is out On Wed, Jul 16, 2014 at 11:01 AM, Dallas Warren dallas.war...@monash.edu wrote: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Switch on periodic image in VMD and you will that it is not a problem at all. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -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 RINU KHATTRI Sent: Wednesday, 16 July 2014 3:24 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Error in system_inflate.gro coordinates does not match hello gromacs users i saw in vmd system.gro its little bit ok very small fragment of protein is out but in shrinkage.gro file box and protein is separated ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include strong_posre.itp #endif ; Include ligand topology #include drag.itp ; Include POPC chain topology #include popc.itp ; Include water topology #include gromos53a6_lipid.ff/spc.itp my topology file kindly help thanks in advance On Wed, Jul 16, 2014 at 10:20 AM, RINU KHATTRI nickname.mi...@gmail.com wrote: hello every one i am working on complex with popc membrane after visualization of minimize structure (after solvation and addition of ions 14 cl-) in VMD i saw protein is moving out em.gro from the lipid membrane i dont know how to resolve it help On Tue, Jul 15, 2014 at 3:42 PM, RINU KHATTRI nickname.mi...@gmail.com wrote: hello everyone now i got the minimize structure after addition of water and ions (14 cl-) i have been select the genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA - nname CL -nn 14 13 th option sol in out put how can i analyze my structure means is it ok or not because next step is equilibration kindly help On Sat, Jul 12, 2014 at 2:48 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/11/14, 3:18 AM, RINU KHATTRI wrote: hello i am following the lysozyme tutorial editconf -f system_shrink20.gro -o newbox.gro -bt dodecahedron -d 1.0 Don't alter the box like this; it's totally nonsensical. solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro but after running second command i got error solvate command not found gmx solvate is also not working The tutorial corresponds to version 5.0; if you're using an older version, the command is called genbox. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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
Re: [gmx-users] PRODRG
Dear all, I was using PRODRG for my protein ligand Simulations, Later, I came across the issues of PRODRG topologies on atom charges, and i have been tryiing to correct these problems. I couldnt use ATB since it gives topopology only for GROMOS96 53a5 and 53a6 force field whereas i need for GROMOS96 43a1. There is a program - ITP Adjuster, an utiltity to correct these charges. Journal of Chemistry - Volume 2013 (2013), Article ID 803151, 6 pages ITP Adjuster 1.0: A New Utility Program to Adjust Charges in the Topology Files Generated by the PRODRG Server. http://dx.doi.org/10.1155/2013/803151 **Is it wise to use this program to correct the PRODRG output ? And how to validate my topology files, Please Help me. Thanks in advance ** *Yours Sincerely,* *B. Sarath Kumar,* *PhD Student**,* *Centre for Biotechnology,* *Anna University, Chennai-25.* -- 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.
