Re: [gmx-users] How to examine our created topology
Dear Justin, I simulate 2,6 dimethylpyridine (lutidine), C7H9N. I use ''gromos43a1'' force field, and I have taken the charges on atoms from Gaussian software. By manipulating charges on the atoms I can get better agreement with experiment for the bulk, but then I loose it's aqueous properties (mixture of water-lutidine). How to overcome this problem? Actually your suggestion ''but the relative contributions of these terms depend on the chemical nature of the molecule(s) involved'' is not clear for me. Best regards - Faezeh Pousaneh Department of Theoretical Physics KTH Royal Institute of Technology AlbaNova University Center SE-106 91 Stockholm, Sweden On Sun, Feb 15, 2015 at 2:04 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/14/15 5:21 AM, Faezeh Pousaneh wrote: Dear expert, I have created topology for an unstudied (simulation) molecule, and I can run it successfully. 1- How many or which quantities at least must be checked with experiment to become sure of the created topology? and if we find some difference with experiment, to what percent this differences can be acceptable? (for instance, if the experimental value of the density is 920 kg/m^3, is 1000 kg/m^3 OK?). That's a fairly large difference. Typically agreement for bulk properties like these is 1-2% deviation for good force fields. 2- If we intend to improve the differences with the experimental values, what are the best ways? is changing slightly the charges on the atoms can be a good way (let us say we correctly have defined bonds, angels, ect according to the force filed)? The real answer comes from what the force field parametrization protocol should be. What force field are you using? What did the developers do to parametrize the existing compounds in the force field? For obtaining correct condensed phase properties, charges and LJ parameters are often tuned, but the relative contributions of these terms depend on the chemical nature of the molecule(s) involved. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Peptide-membrane simulation force field parameters
Thanks Justin for the reply and suggestions. I have more of less similar functional groups as that of the amino acid side chains. Yes, I have figured out some chemical analogy to parametrize the residues. Tarak On Wed, Feb 4, 2015 at 6:51 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/4/15 2:28 AM, tarak karmakar wrote: Dear All, I need a suggestion related to simulation of peptide-membrane system. Are CGenFF parameters (from ParamChem) for peptide analogues good enough to couple with Charmm36 parameters for the lipids in a membrane? (provided very low charge and param penalties) The protein force field is highly optimized, and we generally recommend against trying to shoehorn CGenFF parameters into it. Low penalties just indicate that we cover the chemical space reasonably well in the force field, but that's not necessarily an indicator that those parameters will properly represent a protein moiety. What you have to remember about generalized force fields (CGenFF, GAFF, etc) is that transferability comes at the expense of accuracy. What kind of unnatural residue(s) do you have? Can it be parametrized by analogy from existing functional groups without going to CGenFF? I would recommend relying on the protein force field as much as possible. If you have to derive anything via CGenFF, absolutely run the gamut of normal parameter validation before relying on the parameters for production simulations. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Umbrella sampling restraining potential
On 2/14/15 7:56 PM, Agnivo Gosai wrote: Dear Users The PMF generated by umbrella sampling of my system appears to be converged and the calculated free energy of binding is close to that in published literature. I believe a necessary check for the convergence is the overlap and smoothness of the histograms generated from sampling of the reaction coordinate. Earlier I discussed in the forum regarding my histogram spacing and smoothness. Dr. Lemkul had then pointed out the rocky nature of many histograms and the inadequate overlaps. previous post : http://comments.gmane.org/gmane.science.biology.gromacs.user/74659 For my system there is no experimental study and I am resorting to trial and error. My pull force constant is 1000 kJ/mol/nm^2 whereas the only literature doing a MD study of my system ( with slightly different pulling coordinates) uses a very high force constant of 12600 kJ/mol/nm^2 and they have provided no explanation for this. I have increased simulation time of my windows from 1 ns to 10 ns and I am thinking of using a higher force constant in one half of my windows where the pulled group is closer to the reference group and use a lesser potential in the rest of the windows. However I am declined to use the 12600 units of force constant as it is very high and there is no validation. I found some literature using 1000 - 10,000 kJ/mol/nm^2 force constants for proteins. Ask the corresponding author of the other paper why they did what they did. Often these values are chosen because they just work in the application. I don't see why you'd be averse to 12,600 but OK with 10,000. They're the same order of magnitude. The point is to get proper overlap; if you can't achieve that with simply adding a few more windows, then you have to increase the force constant, which may be very high for regions of the reaction coordinate that are unfavorable. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] error: Atom 1 in multiple Energy Mon. groups
thank you so I have to run different times !? On Sun, Feb 15, 2015 at 5:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/15/15 9:12 AM, nazli kashani javid wrote: Thank you very much. what do you mean of multiple energy evaluations ? do you mean I should change my .mdp file like this: energygrps = chaina chainb chainc chaind is it ok? This will give you nonbonded energy decomposition of: A-B A-C A-D B-C B-D C-D e.g. all possible (non-redundant) combinations of individual chains. if I want to calculate interaction energy between ac and bd chains, what should I do? Then you need groups that are chains AC and chains BD in two groups. -Justin could you help me with more details about .mdp and .ndx files? On Sun, Feb 15, 2015 at 5:23 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/15/15 8:51 AM, nazli kashani javid wrote: Hi all I want to calculate interaction energy of my protein that includes 4 individual chains(a,b,c and d). at first I define an index file. It contains: [ chaina ] 1234 ...454 [ chainb ] 455 456 457 ...919 [ chainc ] 920 921 922 1373 [ chaind ] 1374 1375 1376 1838 [ chainsab ] 123919 [ chainsac ] 123 ...4549201373 [ chainsad ] .. [ chainsbc ] . [ chainsbd ] .. [ chainscd ] [ chainsabc] 123 1373 [ chainsacd ] 123 .454 920 ...1838 [ chainsabd ] .. [ chainsbcd ] I add these groups to .mdp file as following: energygrps = chaina chainb chainc chaind chainsab chainsac chainsad chainsbc chainsbd chainscd chainsabc chainsacd chainsabd chainsbcd when I use grompp command ( grompp -f md.mdp -c npt.gro -p topol.top -n chains.ndx -o mda.tpr) , and face with this error : Fatal error: Atom 1 in multiple Energy Mon. groups (1 and 5) For more information and tips for troubleshooting, please check the GROMACS dose my index file need any modifications? is there any wrong with my mdp file? how could I solve my problem? You can't have overlapping groups. You'll have to do multiple energy evaluations to achieve what you want. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] error: Atom 1 in multiple Energy Mon. groups
thanks, that's very kind of you. On Sun, Feb 15, 2015 at 6:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/15/15 9:29 AM, nazli kashani javid wrote: thank you so I have to run different times !? For any given simulation, you just use mdrun -rerun as many times as needed, with whatever groups are of interest. Interaction energies are just post-processing measures, really. They can be specified during the run or after the fact. -Justin On Sun, Feb 15, 2015 at 5:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/15/15 9:12 AM, nazli kashani javid wrote: Thank you very much. what do you mean of multiple energy evaluations ? do you mean I should change my .mdp file like this: energygrps = chaina chainb chainc chaind is it ok? This will give you nonbonded energy decomposition of: A-B A-C A-D B-C B-D C-D e.g. all possible (non-redundant) combinations of individual chains. if I want to calculate interaction energy between ac and bd chains, what should I do? Then you need groups that are chains AC and chains BD in two groups. -Justin could you help me with more details about .mdp and .ndx files? On Sun, Feb 15, 2015 at 5:23 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/15/15 8:51 AM, nazli kashani javid wrote: Hi all I want to calculate interaction energy of my protein that includes 4 individual chains(a,b,c and d). at first I define an index file. It contains: [ chaina ] 1234 ...454 [ chainb ] 455 456 457 ...919 [ chainc ] 920 921 922 1373 [ chaind ] 1374 1375 1376 1838 [ chainsab ] 123919 [ chainsac ] 123 ...4549201373 [ chainsad ] .. [ chainsbc ] . [ chainsbd ] .. [ chainscd ] [ chainsabc] 123 1373 [ chainsacd ] 123 .454 920 ...1838 [ chainsabd ] .. [ chainsbcd ] I add these groups to .mdp file as following: energygrps = chaina chainb chainc chaind chainsab chainsac chainsad chainsbc chainsbd chainscd chainsabc chainsacd chainsabd chainsbcd when I use grompp command ( grompp -f md.mdp -c npt.gro -p topol.top -n chains.ndx -o mda.tpr) , and face with this error : Fatal error: Atom 1 in multiple Energy Mon. groups (1 and 5) For more information and tips for troubleshooting, please check the GROMACS dose my index file need any modifications? is there any wrong with my mdp file? how could I solve my problem? You can't have overlapping groups. You'll have to do multiple energy evaluations to achieve what you want. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit
[gmx-users] lower Area per lipid for DPPC with CHARMM36
Dear All, All atom simulation of DPPC bilayer (128 lipids) is resulting a low area per lipid (sliding down from ~58 to ~54 in 4 ns NPT). I'm performing the simulation in gromacs-5.0.4 with the charmm36 force field parameters for the lipid molecules. The NPT.mdp is pasted bellow, - title= NPT production for cxcr_WT ; Parameters describing the details of the NVT simulation protocol integrator= md; Algorithm (md = molecular dynamics [leap-frog integrator]; md-vv = md using velocity verlet; sd = stochastic dynamics) dt= 0.002; Time-step (ps) nsteps= 500; Number of steps to run (0.002 * 50 = 1 ns) ; Parameters controlling output writing nstxout= 1; Write coordinates to output .trr file every 2 ps nstvout= 1; Write velocities to output .trr file every 2 ps nstenergy= 1; Write energies to output .edr file every 2 ps nstlog= 1; Write output to .log file every 2 ps ; Parameters describing neighbors searching and details about interaction calculations ns_type= grid; Neighbor list search method (simple, grid) nstlist= 5; Neighbor list update frequency (after every given number of steps) rlist= 1.2; Neighbor list search cut-off distance (nm) rlistlong = 1.4 rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) vdwtype = switch rvdw = 1.2 ; short-range van der Waals cutoff (in nm) rvdw_switch = 0.8 pbc= xyz; Direction in which to use Perodic Boundary Conditions (xyz, xy, no) ; Parameters for treating bonded interactions continuation= no; Whether a fresh start or a continuation from a previous run (yes/no) constraint_algorithm = LINCS; Constraint algorithm (LINCS / SHAKE) constraints= all-bonds; Which bonds/angles to constrain (all-bonds / hbonds / none / all-angles / h-angles) lincs_iter= 1; Number of iterations to correct for rotational lengthening in LINCS (related to accuracy) lincs_order= 4; Highest order in the expansion of the constraint coupling matrix (related to accuracy) ; Parameters for treating electrostatic interactions coulombtype= PME; Long range electrostatic interactions treatment (cut-off, Ewald, PME) pme_order= 4; Interpolation order for PME (cubic interpolation is represented by 4) fourierspacing= 0.16; Maximum grid spacing for FFT grid using PME (nm) ; Temperature coupling parameters tcoupl= Nose-Hoover; Modified Berendsen thermostat using velocity rescaling tc-grps= DPPC SOL_Ion; Define groups to be coupled separately to temperature bath tau_t= 0.50.5; Group-wise coupling time constant (ps) ref_t= 300300; Group-wise reference temperature (K) ; Pressure coupling parameters pcoupl= Parrinello-Rahman; Pressure coupler used under NPT conditions pcoupltype= semiisotropic; Isotropic scaling in the x-y direction, independent of the z direction tau_p= 5.0; Coupling time constant (ps) ref_p= 1.01.0; Reference pressure for coupling, x-y, z directions (bar) compressibility = 4.5e-54.5e-5; Isothermal compressibility (bar^-1) ; Miscellaneous control parameters ; Dispersion correction DispCorr= EnerPres; Dispersion corrections for Energy and Pressure for vdW cut-off ; Initial Velocity Generation gen_vel= no; Velocity is read from the previous run ; Centre of mass (COM) motion removal relative to the specified groups nstcomm= 1; COM removal frequency (steps) comm_mode= Linear; Remove COM translation (linear / angular / no) comm_grps= DPPC SOL_Ion; COM removal relative to the specified groups --- Any suggestions would be appreciated. Thanks, Tarak -- 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] error: Atom 1 in multiple Energy Mon. groups
Hi all I want to calculate interaction energy of my protein that includes 4 individual chains(a,b,c and d). at first I define an index file. It contains: [ chaina ] 1234 ...454 [ chainb ] 455 456 457 ...919 [ chainc ] 920 921 922 1373 [ chaind ] 1374 1375 1376 1838 [ chainsab ] 123919 [ chainsac ] 123 ...4549201373 [ chainsad ] .. [ chainsbc ] . [ chainsbd ] .. [ chainscd ] [ chainsabc] 123 1373 [ chainsacd ] 123 .454 920 ...1838 [ chainsabd ] .. [ chainsbcd ] I add these groups to .mdp file as following: energygrps = chaina chainb chainc chaind chainsab chainsac chainsad chainsbc chainsbd chainscd chainsabc chainsacd chainsabd chainsbcd when I use grompp command ( grompp -f md.mdp -c npt.gro -p topol.top -n chains.ndx -o mda.tpr) , and face with this error : Fatal error: Atom 1 in multiple Energy Mon. groups (1 and 5) For more information and tips for troubleshooting, please check the GROMACS dose my index file need any modifications? is there any wrong with my mdp file? how could I solve my problem? any help is appreciated. -- 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] lower Area per lipid for DPPC with CHARMM36
On 2/15/15 7:39 AM, tarak karmakar wrote: Dear All, All atom simulation of DPPC bilayer (128 lipids) is resulting a low area per lipid (sliding down from ~58 to ~54 in 4 ns NPT). I'm performing the simulation in gromacs-5.0.4 with the charmm36 force field parameters for the lipid molecules. The NPT.mdp is pasted bellow, We've been discussing this exact topic in another thread for days... Your .mdp settings are wrong. http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM -Justin - title= NPT production for cxcr_WT ; Parameters describing the details of the NVT simulation protocol integrator= md; Algorithm (md = molecular dynamics [leap-frog integrator]; md-vv = md using velocity verlet; sd = stochastic dynamics) dt= 0.002; Time-step (ps) nsteps= 500; Number of steps to run (0.002 * 50 = 1 ns) ; Parameters controlling output writing nstxout= 1; Write coordinates to output .trr file every 2 ps nstvout= 1; Write velocities to output .trr file every 2 ps nstenergy= 1; Write energies to output .edr file every 2 ps nstlog= 1; Write output to .log file every 2 ps ; Parameters describing neighbors searching and details about interaction calculations ns_type= grid; Neighbor list search method (simple, grid) nstlist= 5; Neighbor list update frequency (after every given number of steps) rlist= 1.2; Neighbor list search cut-off distance (nm) rlistlong = 1.4 rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) vdwtype = switch rvdw = 1.2 ; short-range van der Waals cutoff (in nm) rvdw_switch = 0.8 pbc= xyz; Direction in which to use Perodic Boundary Conditions (xyz, xy, no) ; Parameters for treating bonded interactions continuation= no; Whether a fresh start or a continuation from a previous run (yes/no) constraint_algorithm = LINCS; Constraint algorithm (LINCS / SHAKE) constraints= all-bonds; Which bonds/angles to constrain (all-bonds / hbonds / none / all-angles / h-angles) lincs_iter= 1; Number of iterations to correct for rotational lengthening in LINCS (related to accuracy) lincs_order= 4; Highest order in the expansion of the constraint coupling matrix (related to accuracy) ; Parameters for treating electrostatic interactions coulombtype= PME; Long range electrostatic interactions treatment (cut-off, Ewald, PME) pme_order= 4; Interpolation order for PME (cubic interpolation is represented by 4) fourierspacing= 0.16; Maximum grid spacing for FFT grid using PME (nm) ; Temperature coupling parameters tcoupl= Nose-Hoover; Modified Berendsen thermostat using velocity rescaling tc-grps= DPPC SOL_Ion; Define groups to be coupled separately to temperature bath tau_t= 0.50.5; Group-wise coupling time constant (ps) ref_t= 300300; Group-wise reference temperature (K) ; Pressure coupling parameters pcoupl= Parrinello-Rahman; Pressure coupler used under NPT conditions pcoupltype= semiisotropic; Isotropic scaling in the x-y direction, independent of the z direction tau_p= 5.0; Coupling time constant (ps) ref_p= 1.01.0; Reference pressure for coupling, x-y, z directions (bar) compressibility = 4.5e-54.5e-5; Isothermal compressibility (bar^-1) ; Miscellaneous control parameters ; Dispersion correction DispCorr= EnerPres; Dispersion corrections for Energy and Pressure for vdW cut-off ; Initial Velocity Generation gen_vel= no; Velocity is read from the previous run ; Centre of mass (COM) motion removal relative to the specified groups nstcomm= 1; COM removal frequency (steps) comm_mode= Linear; Remove COM translation (linear / angular / no) comm_grps= DPPC SOL_Ion; COM removal relative to the specified groups --- Any suggestions would be appreciated. Thanks, Tarak -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
Re: [gmx-users] error: Atom 1 in multiple Energy Mon. groups
On 2/15/15 9:29 AM, nazli kashani javid wrote: thank you so I have to run different times !? For any given simulation, you just use mdrun -rerun as many times as needed, with whatever groups are of interest. Interaction energies are just post-processing measures, really. They can be specified during the run or after the fact. -Justin On Sun, Feb 15, 2015 at 5:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/15/15 9:12 AM, nazli kashani javid wrote: Thank you very much. what do you mean of multiple energy evaluations ? do you mean I should change my .mdp file like this: energygrps = chaina chainb chainc chaind is it ok? This will give you nonbonded energy decomposition of: A-B A-C A-D B-C B-D C-D e.g. all possible (non-redundant) combinations of individual chains. if I want to calculate interaction energy between ac and bd chains, what should I do? Then you need groups that are chains AC and chains BD in two groups. -Justin could you help me with more details about .mdp and .ndx files? On Sun, Feb 15, 2015 at 5:23 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/15/15 8:51 AM, nazli kashani javid wrote: Hi all I want to calculate interaction energy of my protein that includes 4 individual chains(a,b,c and d). at first I define an index file. It contains: [ chaina ] 1234 ...454 [ chainb ] 455 456 457 ...919 [ chainc ] 920 921 922 1373 [ chaind ] 1374 1375 1376 1838 [ chainsab ] 123919 [ chainsac ] 123 ...4549201373 [ chainsad ] .. [ chainsbc ] . [ chainsbd ] .. [ chainscd ] [ chainsabc] 123 1373 [ chainsacd ] 123 .454 920 ...1838 [ chainsabd ] .. [ chainsbcd ] I add these groups to .mdp file as following: energygrps = chaina chainb chainc chaind chainsab chainsac chainsad chainsbc chainsbd chainscd chainsabc chainsacd chainsabd chainsbcd when I use grompp command ( grompp -f md.mdp -c npt.gro -p topol.top -n chains.ndx -o mda.tpr) , and face with this error : Fatal error: Atom 1 in multiple Energy Mon. groups (1 and 5) For more information and tips for troubleshooting, please check the GROMACS dose my index file need any modifications? is there any wrong with my mdp file? how could I solve my problem? You can't have overlapping groups. You'll have to do multiple energy evaluations to achieve what you want. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to examine our created topology
On 2/15/15 9:39 AM, Faezeh Pousaneh wrote: Dear Justin, I simulate 2,6 dimethylpyridine (lutidine), C7H9N. I use ''gromos43a1'' force field, and I have taken the charges on atoms from Gaussian software. By manipulating charges on the atoms I can get better agreement with experiment for the bulk, but then I loose it's aqueous properties (mixture of water-lutidine). How to overcome this problem? Save yourself some time. This compound is already available from ATB. http://compbio.biosci.uq.edu.au/atb/molecule.py?molid=999outputType=topatbVersion=v2TopffVersion=54A7format=GROMACS They provide the experimental hydration free energy, which should (along with density) be a main point for validation of the model. Actually your suggestion ''but the relative contributions of these terms depend on the chemical nature of the molecule(s) involved'' is not clear for me. It's inherently a generic statement, but it makes you think about the chemical nature of the problem. Given I didn't know what your molecule was, I couldn't be specific. If you have something with a bulky alkyl chain, you're probably not going to spend a lot of time on charges, because LJ will dominate. Conversely, something that is highly polar or charged would require some pretty good charges. Ultimately, everything in a force field is a balance of all the contributions, so all can and should be tuned and scrutinized. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Semiisotropic pressure coupling
Dear Justin, I have sent the files to you at your vt.edu Thanks, sxn On Sun, Feb 15, 2015 at 7:59 AM, Justin Lemkul jalem...@vt.edu wrote: On 2/14/15 9:52 PM, shivangi nangia wrote: Hello Justin, I ran the simulation for 100 ns and I still get low APL at 303 K, 0.58 nm^2 :( That outcome is inconsistent with everything I have seen from our own internal testing and published works that use GROMACS. Something else must be up. If you post all of your input files somewhere that I can download them, I'll try to take a look. -Justin Thanks in advance. sxn On Fri, Feb 13, 2015 at 5:03 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/13/15 5:00 PM, shivangi nangia wrote: Hello All, Thank you all for you input. I now have access to GROMACS 5.0. On using the recommended settings, the APL is sill dropping within 3 ns of the simulation. 3 ns is orders of magnitude too short to draw any conclusions. Simulate out to 100 ns and we'll talk :) I only say this because I know the APL can be reproduced with the settings I gave in CHARMM and GROMACS with very close agreement. snip nstlist = 1 Yikes! You're losing a ton of performance here (though check the log to make sure Verlet adjusted this to something more suitable). Setting nstlist = 1 is only for energy minimization. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Semiisotropic pressure coupling
On 2/15/15 11:32 AM, shivangi nangia wrote: Sorry about that. Here it is: https://drive.google.com/file/d/0B9SJqGLyLrwVcThWbEthaFo3SGc/view?usp=sharing So this is actually a system in which a peptide is peripherally bound to a POPC membrane. That complicates things significantly. Not only is it less straightforward to calculate APL, but you have to consider that the protein itself perturbs the lipid properties. If you want to evaluate the validity of the parameters, you need to be running a simulation of a pure POPC membrane. How have you calculated APL? Have you run a pure POPC membrane simulation? These are the only things worth spending time on. Otherwise, all you're seeing is either (1) a problem with how you're calculating APL and/or (2) effects of the peptide. -Justin Shivangi Nangia, Ph. D Postdoctoral Research Associate Department of Molecular and Cell Biology University of Connecticut On Sun, Feb 15, 2015 at 11:13 AM, Justin Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: On 2/15/15 10:53 AM, shivangi nangia wrote: Hello Justin, Please find the files in the link below: https://drive.google.com/__folderview?id=__0B9SJqGLyLrwVa3MxME1IYjZJS0k__usp=sharing https://drive.google.com/folderview?id=0B9SJqGLyLrwVa3MxME1IYjZJS0kusp=sharing It also contains a readme file. Thanks so much for all your help. Please let me know if you need anything else. Please upload a tarball with all the files so I don't have to download dozens of things individually. -Justin Thanks a lot, Shivangi Nangia, Ph. D Postdoctoral Research Associate Department of Molecular and Cell Biology University of Connecticut On Sun, Feb 15, 2015 at 7:59 AM, Justin Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: On 2/14/15 9:52 PM, shivangi nangia wrote: Hello Justin, I ran the simulation for 100 ns and I still get low APL at 303 K, 0.58 nm^2 :( That outcome is inconsistent with everything I have seen from our own internal testing and published works that use GROMACS. Something else must be up. If you post all of your input files somewhere that I can download them, I'll try to take a look. -Justin Thanks in advance. sxn On Fri, Feb 13, 2015 at 5:03 PM, Justin Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: On 2/13/15 5:00 PM, shivangi nangia wrote: Hello All, Thank you all for you input. I now have access to GROMACS 5.0. On using the recommended settings, the APL is sill dropping within 3 ns of the simulation. 3 ns is orders of magnitude too short to draw any conclusions. Simulate out to 100 ns and we'll talk :) I only say this because I know the APL can be reproduced with the settings I gave in CHARMM and GROMACS with very close agreement. snip nstlist = 1 Yikes! You're losing a ton of performance here (though check the log to make sure Verlet adjusted this to something more suitable). Setting nstlist = 1 is only for energy minimization. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu mailto:jalemkul@outerbanks.__umaryland.edu mailto:jalem...@outerbanks.umaryland.edu | (410) 706-7441 tel:%28410%29%20706-7441 tel:%28410%29%20706-7441 http://mackerell.umaryland.edu/~jalemkul http://mackerell.umaryland.__edu/~jalemkul http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list *
[gmx-users] NVT step
Dear Justin,I studied your toturial (KALP15 in DPPC).I'm simulating a drug at dppc, at nvt step i used this command: mdrun -deffnm nvt -v , but i gave this error: Fatal error: 1 particles communicated to PME node 1 are more than 2/3 times the cut-off outof the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check theGROMACS website at http://www.gromacs.org/Documentation/Errors what must i do? Many thanks, Mrs. Mahdavi -- 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] electric fields
Hi all, I need to apply magnetic and also alternating electric field to my system, but I can't find any options. Can anyone help me? thanks! On Fri, Feb 13, 2015 at 8:44 PM, mah maz mahma...@gmail.com wrote: Dear all, What kinds of electric and magnetic fields are available in gromacs? Are there any commands for discontinuous(alternating) fields? thank you! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] electric fields
On 2/15/15 12:31 PM, mah maz wrote: Hi all, I need to apply magnetic and also alternating electric field to my system, but I can't find any options. Can anyone help me? Probably because those options don't exist. Constant electric fields are described in manual section 7.3.26 (conveniently entitled Electric fields). Beyond that, if it's not in the manual, it's not in GROMACS. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Semiisotropic pressure coupling
On 2/15/15 1:02 PM, shivangi nangia wrote: Dear Justin, Thanks for the continuous help. Since I have done reverse CG, The CG POPC was equilibrated alone anisotropically, The APL was fine there. On reverse CG and NVT its still fine, it only after NPT it starts dropping. Of course it's fine during NVT - the box can't change so the area is constant. I am calculating APL as (2*Lx*Ly)/(No. of Lipids). That's only valid for pure, symmetric membranes. You have a protein embedded in one leaflet, so this method is wrong. You mentioned to get gull force field from your site, is it here: http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs Yes, that's the right place. On unzipping this I see POPC is an .trp entry. If there is some other database, kindly point it out to me. What I'm telling you is to use those force field files to (1) verify that your POPC parameters are right (they should be) and (2) you'll have the right protein topology (there are different bonded parameters that will affect protein dynamics). Again, I must emphasize - troubleshooting the APL of this system with respect to the known APL of pure POPC is pointless. You have a protein that convolutes (and potentially changes) everything. If you want to simulate pure POPC to verify that things are fine, do that. But taking more time on any perceived discrepancies here is not productive. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Can only find GPU'S on first node
Have you tried using: mpirun -np (number of mpi-processes total) -npernode (number of gpus per node) . when you execute mdrun? Not sure if it will do the trick, but it looks like it may work. What that command should do it limit the number of mpi-process to the number of gpus (so that each node uses all of the gpus, one per mpi process). -Micholas Hey Micholas, works perfectly. Thanks. Wes -- 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] electric fields
Dear Justin, David Thank you for your reply. I have also seen not implemented yet as Justin said. David, I hope your option E-xt works. But still I don't know if I should supply its parameters the same as E-x or it would be different. Thanks a lot! On Sun, Feb 15, 2015 at 9:01 PM, mah maz mahma...@gmail.com wrote: Hi all, I need to apply magnetic and also alternating electric field to my system, but I can't find any options. Can anyone help me? thanks! On Fri, Feb 13, 2015 at 8:44 PM, mah maz mahma...@gmail.com wrote: Dear all, What kinds of electric and magnetic fields are available in gromacs? Are there any commands for discontinuous(alternating) fields? thank you! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] electric fields
On 2015-02-15 20:49, mah maz wrote: Dear Justin, David Thank you for your reply. I have also seen not implemented yet as Justin said. David, I hope your option E-xt works. But still I don't know if I should supply its parameters the same as E-x or it would be different. The field has the form of a gaussian laser pulse E(t) = E0 exp ( -(t-t0)^2/(2 sigma^2) ) cos(omega (t-t0)) the four parameters are set like E-x = 1 E0 0 E-xt = omega t0 sigma In the special case that sigma = 0 the exponential term is disregarded and only the cosine term is used. More details in Carl Caleman and David van der Spoel: Picosecond Melting of Ice by an Infrared Laser Pulse - A Simulation Study Angew. Chem. Intl. Ed. 47 pp. 1417-1420 (2008) Thanks a lot! On Sun, Feb 15, 2015 at 9:01 PM, mah maz mahma...@gmail.com wrote: Hi all, I need to apply magnetic and also alternating electric field to my system, but I can't find any options. Can anyone help me? thanks! On Fri, Feb 13, 2015 at 8:44 PM, mah maz mahma...@gmail.com wrote: Dear all, What kinds of electric and magnetic fields are available in gromacs? Are there any commands for discontinuous(alternating) fields? thank you! -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] electric fields
On 2015-02-15 18:35, Justin Lemkul wrote: On 2/15/15 12:31 PM, mah maz wrote: Hi all, I need to apply magnetic and also alternating electric field to my system, but I can't find any options. Can anyone help me? Probably because those options don't exist. Constant electric fields are described in manual section 7.3.26 (conveniently entitled Electric fields). Beyond that, if it's not in the manual, it's not in GROMACS. -Justin Not entirely correct. Alternating electric fields work fine. You need to supply both E-x and E-xt fields in the mdp file. Magnetic fields we don't have. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] electric fields
On 2/15/15 1:56 PM, David van der Spoel wrote: On 2015-02-15 18:35, Justin Lemkul wrote: On 2/15/15 12:31 PM, mah maz wrote: Hi all, I need to apply magnetic and also alternating electric field to my system, but I can't find any options. Can anyone help me? Probably because those options don't exist. Constant electric fields are described in manual section 7.3.26 (conveniently entitled Electric fields). Beyond that, if it's not in the manual, it's not in GROMACS. -Justin Not entirely correct. Alternating electric fields work fine. You need to supply both E-x and E-xt fields in the mdp file. Then perhaps it's time to update the documentation for E-[xyz]t to something other than not implemented yet :) -Justin Magnetic fields we don't have. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] NVT step
On 2/15/15 12:44 PM, asasa qsqs wrote: Dear Justin,I studied your toturial (KALP15 in DPPC).I'm simulating a drug at dppc, at nvt step i used this command: mdrun -deffnm nvt -v , but i gave this error: Fatal error: 1 particles communicated to PME node 1 are more than 2/3 times the cut-off outof the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check theGROMACS website at http://www.gromacs.org/Documentation/Errors what must i do? http://www.gromacs.org/Documentation/Terminology/Blowing_Up -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] counting dihedral transitions not working with gmx angle (Mark Abraham)
Hi, As far as I can see, that should work... Looks like a bug, but I can't see why. If you can reproduce it with a small piece of your trajectory, please make a tarball of the input files and file an issue at http://redmine.gromacs.org and I'll take a look. Thanks, Mark On Feb 13, 2015 4:51 PM, Cristi Amariei fenix...@hotmail.it wrote: Here is the line command end the output : (by the way the GROMACS's vertion is 4.6.5 ) g_angle -type dihedral -f 30iso_amber94_323_2-3_pol.xtc -b 7 -od prova -ot t-ptova -oh h-prova -n indicediedri.ndx . Option Filename Type Description -f 30iso_amber94_323_2-3_pol.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt -n indicediedri.ndx InputIndex file -od prova.xvg Output xvgr/xmgr file -ovangaver.xvg Output, Opt. xvgr/xmgr file -ofdihfrac.xvg Output, Opt. xvgr/xmgr file -ott-ptova.xvg Output, Opt! xvgr/xmgr file -ohh-prova.xvg Output, Opt! xvgr/xmgr file -ocdihcorr.xvg Output, Opt. xvgr/xmgr file -or traj.trr Output, Opt. Trajectory in portable xdr format Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint19 Set the nicelevel -b time 7 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -[no]w bool no View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -typeenum dihedral Type of angle to analyse: angle, dihedral, improper or ryckaert-bellemans -[no]all bool no Plot all angles separately in the averages file, in the order of appearance in the index file. -binwidthreal 1 binwidth (degrees) for calculating the distribution -[no]periodic bool yes Print dihedral angles modulo 360 degrees -[no]chandler bool no Use Chandler correlation function (N[trans] = 1, N[gauche] = 0) rather than cosine correlation function. Trans is defined as phi -60 or phi 60. -[no]avercorr bool no Average the correlation functions for the individual angles/dihedrals -acflen int-1 Length of the ACF, default is half the number of frames -[no]normalize bool yes Normalize ACF -P enum 0 Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3 -fitfn enum noneFit function: none, exp, aexp, exp_exp, vac, exp5, exp7, exp9 or erffit -ncskip int0 Skip this many points in the output file of correlation functions -beginfitreal 0 Time where to begin the exponential fit of the correlation function -endfit real -1 Time where to end the exponential fit of the correlation function, -1 is until the end Group 0 ( -CBCACB+CA) has 116 elements Group 1 ( CACB+CA+CB) has 116 elements Group 2 (-CBCACB+CA-) has 232 elements Group 3 ( diedro) has 4 elements Group 4 (diedro2) has 4 elements Select a group: 3 Selected 3: 'diedro' Last frame 1 time 12.000 Found points in the range from 0 to 359 (max 360) angle = -73.7241 angle^2 = 29402 Std. Dev. = 154.812 Order parameter S^2 = 0.973661 The number of frames is 10. thanks Cristi Amariei -- 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] Re;calculating interaction energies of dimers and ligand
Dear Justin, I notice that -rerun option in mdrun. As per your suggestion, i have made a tpr file using energyrps in md.mdp file as like this gmx grompp -f md.mdp -c npt.gro -t npt.cpt -o check.tpr and tried to use mdrun -reun gmx mdrun -rerun check but end up with Can not open file: topol.tpr Dear Justin, I already ran 10 ns without mentioned the energyrps. Now I have added the energyrps in md.mdp file. Should i need to rerun 10 ns again to get the interaction energies? what does mdrun -rerun ? On 2/13/15 7:07 AM, RJ wrote: Dear all, I need to calculate the interaction energy (Column SR LJ SR) of chain A with chain B. Should I need to select the specific interacting residues to between chain A and B ? Also to chain C ( Ligand molecule)?. I used the gmx energy command line but there are index.ndx option to indicate the group of residues so? To get this information printed to the .edr file, you need to do your run with correct energygrps defined. If you didn't do that, create a .tpr file that specifies these groups and re-calculate energies with mdrun -rerun. Also, how do i calculate the interaction energies in nano second time scale ( seems there is no -tu option in gmx energy)? Just convert after the fact in the text file or plotting software. The time unit is always ps in .edr files. -Justin -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Regarding DSSP
Hello all: I am not really sure, what are the various compatibility issues between the do_dssp program of different Gromacs versions and the versions of the DSSP program itself. I am trying to use dssp 2.0.4 and Gromacs 4.5.6. I have used export DSSP=/usr/bin/dssp and then do_dssp - I am getting Fatal error: Failed to execute command: /usr/bin/dssp -na ddMjYR8P ddfm1ecX /dev/null 2 /dev/null. Can someone please enlighten me about this? -- 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] Plz help File input/output error: Cannot write trajectory frame;
Hi I am encountering this error for the second time. The simulation exactly stops at 9 NS with this message. Earlier I have the same problem and now I am have check the disk space and there is around 120 GB free space. Is this could be the system hardware is not compatible or its just the hard disk size. Please help me Program gmx, VERSION 5.0 Source code file: /home/salampradeep/Downloads/gromacs-5.0/src/gromacs/fileio/trnio.c, line: 310 File input/output error: Cannot write trajectory frame; maybe you are out of disk space? For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Yours sincerely Salam Pradeep, Tezpur University, Tezpur, Assam, India -- 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 executing do_dssp in gromacs
Hi Justin, Yes, I have checked the env variables and file is also executable. But still giving fatal error and asking me to specify the dssp version. Aarti On Fri, Feb 13, 2015 at 8:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/13/15 4:41 AM, Aarti rana wrote: Hi, I am new to gromacs and using gromacs 4.6.5 and dssp-2.0.4. To study the secondary structure, when I am running these commands: export DSSP=/usr/local/bin/dssp do_dssp -s md_0_1.tpr -f md_0_1_noPBC.xtc -o dssp.xvg -ver 2 I am getting this error: dssp cmd='/usr/local/bin/dssp -na dd31ZWbc ddI6at3a /dev/null 2 /dev/null' Reading frame 0 time 0.000 Back Off! I just backed up dd31ZWbc to ./#dd31ZWbc.1# ---Program do_dssp, VERSION 4.6.5 Source code file: /build/buildd/gromacs-4.6.5/src/tools/gmx_do_dssp.c, line: 669 Fatal error: Failed to execute command: Try specifying your dssp version with the -ver option. I have already checked many helping sites but couldn't solve it. I have also checked the earlier comments posted here. I don't know how to fix it. Please help me? Is your DSSP environment variable the correct location of the dssp binary and is the dssp binary executable? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- *Happy and Healthy mantra of life : Enjoy what you have now, stop collecting luxuries of life, because an unsatisfied person cannot relish the precious moments of life, stay happy, stay cool, keep smiling, stay away from arguments and controversies.* -- 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] Re;calculating interaction energies of dimers and ligand
Dear Justin, I already ran 10 ns without mentioned the energyrps. Now I have added the energyrps in md.mdp file. Should i need to rerun 10 ns again to get the interaction energies? what does mdrun -rerun ? On 2/13/15 7:07 AM, RJ wrote: Dear all, I need to calculate the interaction energy (Column SR LJ SR) of chain A with chain B. Should I need to select the specific interacting residues to between chain A and B ? Also to chain C ( Ligand molecule)?. I used the gmx energy command line but there are index.ndx option to indicate the group of residues so? To get this information printed to the .edr file, you need to do your run with correct energygrps defined. If you didn't do that, create a .tpr file that specifies these groups and re-calculate energies with mdrun -rerun. Also, how do i calculate the interaction energies in nano second time scale ( seems there is no -tu option in gmx energy)? Just convert after the fact in the text file or plotting software. The time unit is always ps in .edr files. -Justin -- -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
