Re: [gmx-users] Dynamics only for cavity in molecule.
Hi, I have no idea whether that will help. Even if it is better, I am struggling to see that annealing and freeze groups is a useful model, even with frozen solvent. Mark On Fri, 4 Aug 2017 21:40 wrote: > Well, that means that I need to use the group scheme? > Or I can just add solvent and run the same thing? > > > Hi, > > > > I imagine nobody has ever tried with Verlet plus freeze plus annealing, > so > > it could be broken somehow... But frozen atoms around a cavity and no > > electric field from solvent sounds like a model highly unlikely to be > > related to reality... > > > > Mark > > > > On Fri, 4 Aug 2017 18:55 wrote: > > > >> Hello! > >> > >> I want to run dynamics only for a relatively small cavity of my > >> molecule, > >> with all other atoms frozen. For this reason, I also don't use solvent, > >> because it won't move anyway. I run the simulation on GPU (gromacs > >> 5.1.2), > >> i.e. I use the Verlet scheme, pbc = xyz. However, when I start running > >> simulations, I get violent behavior: the molecule immediately falls > >> apart!! I am sure that I just made a silly thing in the parameters, but > >> what is it? Here I attach my dynamics .mdp parameters: > >> > >> > >> define = -DPOSRES > >> integrator = md > >> dt = 0.001 > >> nsteps = 120 > >> > >> nstxout = 1000 > >> nstvout = 1000 > >> nstxtcout = 1000 > >> nstlog = 100 > >> nstenergy = 1000 > >> > >> continuation = no > >> constraints= none > >> > >> tcoupl = V-rescale > >> tc_grps = System > >> tau_t = 0.1 > >> ref_t = 0 > >> > >> cutoff-scheme = Verlet > >> ns_type = grid > >> nstlist = 10 > >> rcoulomb = 0.9 > >> rvdw = 0.9 > >> > >> coulombtype = PME > >> pme_order = 4 > >> fourierspacing = 0.16 > >> > >> pbc = xyz > >> gen_vel = no > >> > >> DispCorr = EnerPres > >> > >> ; > >> ; Freezing atoms # this is all the atoms except for the cavity inside > >> ; > >> freezegrps = GroupDyna > >> freezedim = Y Y Y > >> ; > >> ; Heating > >> ; > >> annealing = single > >> annealing_npoints = 2 > >> annealing_time = 0 50 > >> annealing_temp = 0 298 > >> > >> > >> Thank you in advance, > >> Dmitrii. > >> > >> > >> -- > >> 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 or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Dynamics only for cavity in molecule.
Well, that means that I need to use the group scheme? Or I can just add solvent and run the same thing? > Hi, > > I imagine nobody has ever tried with Verlet plus freeze plus annealing, so > it could be broken somehow... But frozen atoms around a cavity and no > electric field from solvent sounds like a model highly unlikely to be > related to reality... > > Mark > > On Fri, 4 Aug 2017 18:55 wrote: > >> Hello! >> >> I want to run dynamics only for a relatively small cavity of my >> molecule, >> with all other atoms frozen. For this reason, I also don't use solvent, >> because it won't move anyway. I run the simulation on GPU (gromacs >> 5.1.2), >> i.e. I use the Verlet scheme, pbc = xyz. However, when I start running >> simulations, I get violent behavior: the molecule immediately falls >> apart!! I am sure that I just made a silly thing in the parameters, but >> what is it? Here I attach my dynamics .mdp parameters: >> >> >> define = -DPOSRES >> integrator = md >> dt = 0.001 >> nsteps = 120 >> >> nstxout = 1000 >> nstvout = 1000 >> nstxtcout = 1000 >> nstlog = 100 >> nstenergy = 1000 >> >> continuation = no >> constraints= none >> >> tcoupl = V-rescale >> tc_grps = System >> tau_t = 0.1 >> ref_t = 0 >> >> cutoff-scheme = Verlet >> ns_type = grid >> nstlist = 10 >> rcoulomb = 0.9 >> rvdw = 0.9 >> >> coulombtype = PME >> pme_order = 4 >> fourierspacing = 0.16 >> >> pbc = xyz >> gen_vel = no >> >> DispCorr = EnerPres >> >> ; >> ; Freezing atoms # this is all the atoms except for the cavity inside >> ; >> freezegrps = GroupDyna >> freezedim = Y Y Y >> ; >> ; Heating >> ; >> annealing = single >> annealing_npoints = 2 >> annealing_time = 0 50 >> annealing_temp = 0 298 >> >> >> Thank you in advance, >> Dmitrii. >> >> >> -- >> 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] error at nvt equilibrium
Dear Sir I am getting the error when I try for *gmx mdrun -deffnm nvt. * I have attached my nvt.mdp. Can anyone help me about it Double sids (1547, 1548) for atom 4837 Double sids (1547, 1548) for atom 4838 Double sids (1547, 1548) for atom 4839 Double sids (1547, 1548) for atom 4840 Double sids (1547, 1548) for atom 4841 Double sids (1547, 1548) for atom 4842 Double sids (1547, 1548) for atom 4843 Double sids (1547, 1548) for atom 4844 Double sids (1547, 1548) for atom 4845 Double sids (1547, 1548) for atom 4846 Double sids (1547, 1548) for atom 4847 Double sids (1547, 1548) for atom 4848 Double sids (1547, 1548) for atom 4849 --- Program gmx mdrun, VERSION 5.1.2 Source code file: /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/topology/invblock.c, line: 98 Fatal error: Double entries in block structure. Item 3963 is in blocks 1548 and 1547 Cannot make an unambiguous inverse block -- *Mohammad Zahidul Hossain Khan Graduate student**Department of Physics* *Email: khan5...@vandals.uidaho.edu * * Skype: parash.khan2* *Cell: +12085967165* -- 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] Dynamics only for cavity in molecule.
Hi, I imagine nobody has ever tried with Verlet plus freeze plus annealing, so it could be broken somehow... But frozen atoms around a cavity and no electric field from solvent sounds like a model highly unlikely to be related to reality... Mark On Fri, 4 Aug 2017 18:55 wrote: > Hello! > > I want to run dynamics only for a relatively small cavity of my molecule, > with all other atoms frozen. For this reason, I also don't use solvent, > because it won't move anyway. I run the simulation on GPU (gromacs 5.1.2), > i.e. I use the Verlet scheme, pbc = xyz. However, when I start running > simulations, I get violent behavior: the molecule immediately falls > apart!! I am sure that I just made a silly thing in the parameters, but > what is it? Here I attach my dynamics .mdp parameters: > > > define = -DPOSRES > integrator = md > dt = 0.001 > nsteps = 120 > > nstxout = 1000 > nstvout = 1000 > nstxtcout = 1000 > nstlog = 100 > nstenergy = 1000 > > continuation = no > constraints= none > > tcoupl = V-rescale > tc_grps = System > tau_t = 0.1 > ref_t = 0 > > cutoff-scheme = Verlet > ns_type = grid > nstlist = 10 > rcoulomb = 0.9 > rvdw = 0.9 > > coulombtype = PME > pme_order = 4 > fourierspacing = 0.16 > > pbc = xyz > gen_vel = no > > DispCorr = EnerPres > > ; > ; Freezing atoms # this is all the atoms except for the cavity inside > ; > freezegrps = GroupDyna > freezedim = Y Y Y > ; > ; Heating > ; > annealing = single > annealing_npoints = 2 > annealing_time = 0 50 > annealing_temp = 0 298 > > > Thank you in advance, > Dmitrii. > > > -- > 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] Dynamics only for cavity in molecule.
Hello! I want to run dynamics only for a relatively small cavity of my molecule, with all other atoms frozen. For this reason, I also don't use solvent, because it won't move anyway. I run the simulation on GPU (gromacs 5.1.2), i.e. I use the Verlet scheme, pbc = xyz. However, when I start running simulations, I get violent behavior: the molecule immediately falls apart!! I am sure that I just made a silly thing in the parameters, but what is it? Here I attach my dynamics .mdp parameters: define = -DPOSRES integrator = md dt = 0.001 nsteps = 120 nstxout = 1000 nstvout = 1000 nstxtcout = 1000 nstlog = 100 nstenergy = 1000 continuation = no constraints= none tcoupl = V-rescale tc_grps = System tau_t = 0.1 ref_t = 0 cutoff-scheme = Verlet ns_type = grid nstlist = 10 rcoulomb = 0.9 rvdw = 0.9 coulombtype = PME pme_order = 4 fourierspacing = 0.16 pbc = xyz gen_vel = no DispCorr = EnerPres ; ; Freezing atoms # this is all the atoms except for the cavity inside ; freezegrps = GroupDyna freezedim = Y Y Y ; ; Heating ; annealing = single annealing_npoints = 2 annealing_time = 0 50 annealing_temp = 0 298 Thank you in advance, Dmitrii. -- 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] MnO2 periodic system
Dear all, I am trying to equilibrate a MnO2 surface (not cluster periodic). After the NVT run, I see that the surface is deformed. I was wondering what else can I add in my nvt.mdp to not encounter this problem? I have mainly followed the examples in the forum for graphene/CNT growth. title = MnO2 in H2O NVT equilibration ; Run parameters integrator = md; leap-frog integrator nsteps = 5 ; 2 * 50 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 50; save coordinates every 0.10 ps nstvout = 50; save velocities every 0.10 ps nstenergy = 50; save energies every 0.10 ps nstlog = 50; update log file every 0.10 ps ; Bond parameters continuation= no; first dynamics run constraint_algorithm= lincs ; holonomic constraints constraints = none ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 10; 20 fs, largely irrelevant with Verlet rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; 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 is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = SOL MnO ; three 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 is off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC periodic-molecules = yes ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 300 ; temperature for Maxwell distribution gen_seed= 18; generate a random seed *Thank you* *Gangotri Dey* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Gmx hbond
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Dear gromacs user I am performing protein ligand complex (t4lysosim) and now i need to analyze JZ4 hydrogen bonding, but when i type Gmx hbondThere is no JZ4 in the list to choose. It is because of i used :Gmx make_ndx -f em.gro -o index.ndxAnd merged the " protein " and " JZ4" groupsIs there anyone help me how to check the hydrogen bond of JZ4 ligand? Thanks in advanceFarial Sent from Yahoo Mail for iPhone -- 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] question about gmx do_dssp
Hi, Isn't that figure what is in the xpm file? Mark On Fri, Aug 4, 2017 at 4:20 PM YanhuaOuyang <15901283...@163.com> wrote: > Hi, >I have run a MD simulation and used gmx do_dssp to calculate the > secondary structure content. The output files are md_dssp.xpm and > scount.xvg. I want to know that each residue belongs to what kind of > secondary structure for each frame. But the scount.xvg output file only > have the number of residues with each secondary structure and the total > secondary structure count as a function of time. So, can I get the > information on "each residue belongs to which kind of secondary structure > for each frame" to draw a figure of " amino acid vs secondary structure" ? > > Best regards, > Ouyang > -- > 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 with dihedral restraints
Hi, You should expect changes, you're not freezing the angles in place. You're making it less energetically favourable for them to change. But if the environment is strong enough, they'll respond to that. Increase kfac by a factor of a thousand and they'll probably not move noticeably. Whether that is a good idea is something you might find out later :-) Mark On Fri, Aug 4, 2017 at 4:16 PM gangotri dey wrote: > Hello! > > I posted a question a few days back and I got a reply but it still does not > work. > > I have a small drug molecule that I would like to compute. I want to > restraint the Ramachandran dihedral angles. I have used the following lines > in the .itp file for the molecule. It was suggested that I increase the > force constant, which I did. However, I still see the change in the > dihedral angles after the NVT, NPT and Production run. I am not sure how > best it can be implemented. > > > > [ dihedral_restraints ] > ; ai ajakal type phi dphi kfac > 698 702 692 691 1 -142.56 0 100 > 719 712 716 698 1 -84.24 0 100 > > 702698716712 150.3766 0 100 > 695691692702 1 -166.8294 0 100 > > > My .mdp file is similar to the one used in the Bevan lab tutorial online. > > > > > *Thank you* > > *Gangotri Dey* > -- > 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 with dihedral restraints
Thank you for the kind reply. I will compute and update in the post. *Thank you* *Gangotri Dey* Postdoctoral Associate Rutgers University New Brunswick Chemistry and Chemical Biology 174 Frelinghuysen Road, Piscataway, NJ 08854 Phone: +16092162254 On Fri, Aug 4, 2017 at 10:31 AM, Mark Abraham wrote: > Hi, > > You should expect changes, you're not freezing the angles in place. You're > making it less energetically favourable for them to change. But if the > environment is strong enough, they'll respond to that. Increase kfac by a > factor of a thousand and they'll probably not move noticeably. Whether that > is a good idea is something you might find out later :-) > > Mark > > On Fri, Aug 4, 2017 at 4:16 PM gangotri dey wrote: > > > Hello! > > > > I posted a question a few days back and I got a reply but it still does > not > > work. > > > > I have a small drug molecule that I would like to compute. I want to > > restraint the Ramachandran dihedral angles. I have used the following > lines > > in the .itp file for the molecule. It was suggested that I increase the > > force constant, which I did. However, I still see the change in the > > dihedral angles after the NVT, NPT and Production run. I am not sure how > > best it can be implemented. > > > > > > > > [ dihedral_restraints ] > > ; ai ajakal type phi dphi kfac > > 698 702 692 691 1 -142.56 0 100 > > 719 712 716 698 1 -84.24 0 100 > > > > 702698716712 150.3766 0 100 > > 695691692702 1 -166.8294 0 100 > > > > > > My .mdp file is similar to the one used in the Bevan lab tutorial online. > > > > > > > > > > *Thank you* > > > > *Gangotri Dey* > > -- > > 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] question about gmx do_dssp
Hi, I have run a MD simulation and used gmx do_dssp to calculate the secondary structure content. The output files are md_dssp.xpm and scount.xvg. I want to know that each residue belongs to what kind of secondary structure for each frame. But the scount.xvg output file only have the number of residues with each secondary structure and the total secondary structure count as a function of time. So, can I get the information on "each residue belongs to which kind of secondary structure for each frame" to draw a figure of " amino acid vs secondary structure" ? Best regards, Ouyang -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Problem with dihedral restraints
Hello! I posted a question a few days back and I got a reply but it still does not work. I have a small drug molecule that I would like to compute. I want to restraint the Ramachandran dihedral angles. I have used the following lines in the .itp file for the molecule. It was suggested that I increase the force constant, which I did. However, I still see the change in the dihedral angles after the NVT, NPT and Production run. I am not sure how best it can be implemented. [ dihedral_restraints ] ; ai ajakal type phi dphi kfac 698 702 692 691 1 -142.56 0 100 719 712 716 698 1 -84.24 0 100 702698716712 150.3766 0 100 695691692702 1 -166.8294 0 100 My .mdp file is similar to the one used in the Bevan lab tutorial online. *Thank you* *Gangotri Dey* -- 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 itp file
You can use this link for ACPYPE: http://webapps.ccpn.ac.uk/acpype/ First, you have to mail the author and then he would give you a user ID and password. On Fri, Aug 4, 2017 at 1:48 AM, Justin Lemkul wrote: > > > On 8/3/17 8:53 AM, Souvik Dey wrote: > >> Yes, I saw the GROMACS website. But my itp file has [atomtypes] first >> followed by [moleculetypes]. So, I am still not getting what is the >> error. >> >> > All [atomtypes] (and more generally, any force field parameters) must > appear before *any* [moleculetype] directives, not just the one to which > the parameters apply. So a topology that introduces parameters must be > #included before any invocation of a [moleculetype]. > > -Justin > > > On Thu, Aug 3, 2017 at 2:52 PM, Souvik Dey wrote: >> >> Yes, using ACPYPE is pretty simple. They have a web server, where you can >>> upload your PDB or MOL2 file, provide the charge and multiplicity and it >>> gives you the output file. >>> >>> On Wed, Aug 2, 2017 at 7:03 PM, Justin Lemkul wrote: >>> >>> On 8/2/17 12:35 PM, Souvik Dey wrote: Hi, > > I just generated an itp file from ACPYPE. However, if I try to add ions > it > shows the following error: > > Fatal error: > Syntax error - File FAD.itp, line 3 > Last line read: > '[ atomtypes ]' > Invalid order for directive atomtypes > > > Can somebody say how do I fix this? > > > This exact situation is described here: http://www.gromacs.org/Documentation/Errors#Invalid_order_fo r_directive_xxx -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. >>> >>> >>> -- >>> Souvik Dey >>> Integrated Science Education & Research Centre >>> Visva Bharati University >>> Santiniketan-731235 >>> West Bengal >>> 8981736643 >>> >>> >> >> >> > -- > == > > 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. > -- Souvik Dey Integrated Science Education & Research Centre Visva Bharati University Santiniketan-731235 West Bengal 8981736643 -- 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] Could not find clayff forcefield
Dear users, I try to implement Clayff forcefield for Kaolinite. I created my force field (I'm not sure about it), but gromacs couldn't find my force field in the directory. Here is my forcefield. ffnonbonded [ atomtypes ] ; name mass chargeptype sigma eps HW 1 1.00800 0.4100A0.0e-01 0.0e-01 ;clayFF_waterhydrogen HO 1 1.00800 0.4250A0.0e-01 0.0e-01 ;clayFF_hydroxylhydrogen OW 8 15.99800-0.8200A3.16557e-01 6.50209e-01 ;ClayFF_wateroxygen OH 8 15.99800-0.9500A3.16557e-01 6.50209e-01 ;ClayFF_hydroxyloxygen OB 8 15.99800-1.0500A3.16557e-01 6.50209e-01 ;ClayFF_bridgingoxygen OBOS 8 15.99800-1.1808A3.16557e-01 6.50209e-01 ;ClayFF_bridgingoxygenoctasub OBTS 8 15.99800-1.1688A3.16557e-01 6.50209e-01 ;ClayFF_bridgingoxygentetrsub OHS 8 15.99800-1.0808A3.16557e-01 6.50209e-01 ;ClayFF_hydroxyloxygensub SI 14 28.08600 2.1000A3.30208e-01 8.0e-06 ;ClayFF_tetrahedralsilicon AO 13 26.98200 1.5750A4.27128e-01 6.0e-06 ;ClayFF_octahedalaluminium AT 13 26.98200 1.5750A3.30206e-01 8.0e-06 ;ClayFF_tetrasubaluminium ffbonded [ bondtypes ] ; ij func b0 kb OW HW 10.1000 554134.9 OH HO 10.1000 554134.9 OHSHO 10.1000 554134.9 [ angletypes ] ; ijk func th0 cth HW OWHW1109.47191.564 AL OHHO1109.47125.52 atomtype.n2t HHW0.4100 1.008 1O 0.100 ;water hydrogen OOW -0.820015.998 2H 0.100H 0.100 ;water oxygen OH2 OH -0.950015.998 1H 0.100 ;hydroxyl oxygen O2 obts -1.1688 15.998 0;bridging oxygen with tetrahedral substitution O1 obss -1.2996 15.998 0 ;bridging oxygen with double substitution OH1 ohs -1.0808 15.998 1 H 0.100 ;hydroxyl hydrogen with substitution Si st2.100028.086 0 ;tetrahedral silicon Al ao1.575026.982 0 ;octahedral aluminium Mg mgo1.360024.305 0 ; octahedral magnisium Na Na1.22.999 0 ;sodium ion forcefield.doc clayff.ff force field forcefield.itp #define _ff_clayff [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 3 yes 0.5 0.5 #include "ffnonbonded.itp" #include "ffbonded.itp" pdb Al0.6494.3333.377 Al3.248.8053.377 Al3.2032.8513.362 Al0.6397.3243.362 Si4.9623.0160.65 Si2.3987.4880.65 Si2.4421.470.653 Si-0.1225.9420.653 O1-0.3343.0982.268 O12.2587.572.268 O10.0415.8392.271 O12.6051.3672.271 O30.0144.4720 O3-1.8854.2597.154 O35.1694.4720 O33.274.2597.154 O32.57800 O30.678-0.2147.154 O32.6058.9450 O30.7068.7317.154 O31.0342.0560.177 O33.6266.5290.177 O31.0526.8480.023 O33.6162.3760.023 OH1-0.3228.6062.304 OH12.2424.1332.304 OH23.831.364.329 OH21.2665.8324.329 OH2-0.9624.1364.35 OH21.6298.6084.35 OH2-0.9617.5354.36 OH21.6023.0634.36 O22.63310.3122.271 OH23.85810.3054.329 OH24.8348.6062.304 OH24.1947.5354.36 O34.8213.0982.268 OH34.1934.1364.35 O36.192.0560.177 O3-1.5296.5290.177 It's to long, Sorry about it, but I really need to find out where is my problem. I put n2t file in directory not in my forcefield subdirectory. Do I need to create any other file for clayff forcefield? Thank you in advece, Golnaz -- 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] The small organic molecule occurred deformation during simulation
Hello, users I’m a novice to study the gromacs program. Now I met some problems which the small molecule occurred deformation when energy minimization was performed. For example, the anthracene molecule became bent in the plane of C-rings, the same as phenol. I want to know whether the situation is normal? In addition, I employed gromos54a7.ff Yours sincerely Yujie liu -- 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] Does gmx distance correct for broken molecules from pbc?
Hi, gmx help distance shows that there are two PBC-related options. Perhaps your answer lies there. Mark On Fri, Aug 4, 2017 at 9:47 AM Ramon Crehuet wrote: > Dear all, > > I have a system composed of a trimeric protein and a double stranded DNA. > I would like to calculate the distance between the center of mass (com) of > the protein and the com of the DNA (I am working with the NVT equilibration > trajectory as an example). I tried: > > > gmx distance -f nvt.trr -s nvt.tpr -select 'com of group Protein plus cog > of group DNA' -xvg none -oall -rmpbc > > This gave distances that seem too long. Then I created a trajectory > removing the PBC: > > gmx trjconv -f em.gro -s em.tpr -o whole.pdb -pbc nojump > gmx trjconv -f nvt.trr -o whole.xtc -s whole.pdb -pbc nojump > > And calculated the distances again: > > gmx distance -f whole.xtc -s whole.pdb -select 'com of group Protein plus > cog of group DNA' -xvg none -oall -rmpbc > > This gives reasonable results, different from the previous call to gmx > distance. In an attempt to avoid calculating the whole.xtc trajectory I > gave a pdb file that doesn't have broken molecules: > > gmx distance -f nvt.trr -s whole.pdb -select 'com of group Protein plus > cog of group DNA' -xvg none -oall -rmpbc > > But this still gives the wrong result. I thought the flag -rmpbc would > make molecules whole, but apparently it doesn't in my case. Is there a way > to calculate the distance directly from the original trajectory? > > > Thanks in advance, > > Ramon > > > > -- > > > Ramon Crehuet > > Cientific Titular (Assistant Professor) > > Institute of Advanced Chemistry of Catalonia IQAC - CSIC > > scholar.google.es/citations?user=PIHmEiwJ > orcid.org/-0002-6687-382X > publons.com/a/1018637/ > twitter.com/rcrehuet > ramoncrehuet.wordpress.com > > Tel. +34 934006116 <+34%20934%2000%2061%2016> > Jordi Girona 18-26 > 08034 Barcelona (Spain) > -- > 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] Does gmx distance correct for broken molecules from pbc?
Dear all, I have a system composed of a trimeric protein and a double stranded DNA. I would like to calculate the distance between the center of mass (com) of the protein and the com of the DNA (I am working with the NVT equilibration trajectory as an example). I tried: gmx distance -f nvt.trr -s nvt.tpr -select 'com of group Protein plus cog of group DNA' -xvg none -oall -rmpbc This gave distances that seem too long. Then I created a trajectory removing the PBC: gmx trjconv -f em.gro -s em.tpr -o whole.pdb -pbc nojump gmx trjconv -f nvt.trr -o whole.xtc -s whole.pdb -pbc nojump And calculated the distances again: gmx distance -f whole.xtc -s whole.pdb -select 'com of group Protein plus cog of group DNA' -xvg none -oall -rmpbc This gives reasonable results, different from the previous call to gmx distance. In an attempt to avoid calculating the whole.xtc trajectory I gave a pdb file that doesn't have broken molecules: gmx distance -f nvt.trr -s whole.pdb -select 'com of group Protein plus cog of group DNA' -xvg none -oall -rmpbc But this still gives the wrong result. I thought the flag -rmpbc would make molecules whole, but apparently it doesn't in my case. Is there a way to calculate the distance directly from the original trajectory? Thanks in advance, Ramon -- Ramon Crehuet Cientific Titular (Assistant Professor) Institute of Advanced Chemistry of Catalonia IQAC - CSIC scholar.google.es/citations?user=PIHmEiwJ orcid.org/-0002-6687-382X publons.com/a/1018637/ twitter.com/rcrehuet ramoncrehuet.wordpress.com Tel. +34 934006116 Jordi Girona 18-26 08034 Barcelona (Spain) -- 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.