[gmx-users] dihedral restraint
Hello all, I am a relatively new user of gromacs. Hence, I am encountering some problem. I am studying few drug molecules onto a metal oxide surface. I would like to constrain the Ramachandran angles. I am using gromacs version 5.4.0. I have added the dihedral restraint angles in the itp file that reads as follows. [ dihedral_restraints ] ; ai ajakal type phi dphi kfac 698 702 692 691 1 163.19 0 1 719 712 716 698 1 -84.24 0 1 712 716 698 689 1 -35.93 0 1 702 692 691 686 1 180.42 0 1 I have read in this forum that there is no need to add any more key words like the previous version in the mdp file. However, the dihedral angles are changing and I am not sure how to restrain them. Is there any part that I am missing. *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] g_clustsize question
On 19/07/17 19:18, antra saxena wrote: Hello, I have a question regarding g_clustsize. I have a multi-peptide system and I want to determine the size of the cluster. As far as I understand, g_clustsize will cluster molecules (with -mol option) within each frame of a trajectory within the cutoff distance specified. With -nc option, I will get the number of clusters formed at a particular time of the simulation but is there a way to know how many molecules are part each cluster? The -o flag will give you a colorful matrix, but it is not so useful for quantitative output unless you set the nlevels accurately. gmx_mpi clustsize -f peptides_only.trr -tu ps -n pep.ndx -cut 0.35 -o -mol -s pep.tpr -pbc Thank, antra -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.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.
[gmx-users] g_clustsize question
Hello, I have a question regarding g_clustsize. I have a multi-peptide system and I want to determine the size of the cluster. As far as I understand, g_clustsize will cluster molecules (with -mol option) within each frame of a trajectory within the cutoff distance specified. With -nc option, I will get the number of clusters formed at a particular time of the simulation but is there a way to know how many molecules are part each cluster? gmx_mpi clustsize -f peptides_only.trr -tu ps -n pep.ndx -cut 0.35 -o -mol -s pep.tpr -pbc Thank, antra -- 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] Using nose-Hoover thermostat with berendsen barostat
Thanks Justin, Mark. Yogesh > On 19-Jul-2017, at 6:42 AM, Justin Lemkul wrote: > > > >> On 7/18/17 9:23 AM, jay patil wrote: >> The reason for using berendsen is: I thought parrinello is sensitive, it's >> not wise to use it while equilibrating. So I was trying to use berendsen for >> equilibration and then production run with parrinello. >> One more thought, my system is not well equilibrated, I know because it got >> disturbed when I pulled one water molecule from solvent region into the >> bilayer. Which disrupted the Bilayer a little bit. Then my system should >> blow up in initial stages only may be because of overlap. Why it is blowing >> up after few nano seconds of simulation. > > Crashes can occur at any time; they're more frequent right at the outset but > bad physics can manifest at any point. If the system ran fine without any > biasing potential, but then you turn on a bias and things become unstable, > you should be troubleshooting whatever restraints you've added, not the > barostat. The pressure instability is a symptom, not a cause. > > -Justin > >> Some insights will be helpful. >> Thanks >> Yogesh >>> On 18-Jul-2017, at 5:37 PM, Mark Abraham wrote: >>> >>> Hi, >>> >>> The more Berendsen you use, the less physics you get ;-) >>> >>> Mark >>> On Tue, 18 Jul 2017 13:44 jay patil wrote: Hi Experts, Can we use nose-Hoover thermostat in combination with berendsen barostat. When I use grompp command, it gives warning berendsen will not give true ensemble, and with -maxwarn 1 option I am able to run the simulation. My doubt is: can we use this combination of thermostat and barostat. Or both should be berendsen. Any suggestion will be helpful. Thanks Yogesh -- 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. > > -- > == > > 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] nitrogen itp file with virtual site
On 7/19/17 9:48 AM, Ali Ahmed wrote: Dear Justin I have checked and tried but still not working, it says ( invalid order for directive atomtypes). Please can you take a look on the following You're missing several required directives. Start by reading Chapter 5 of the manual and the associated tables that show you the order in which things have to appear. Google can also help - the answers are all out there in the archive :) -Justin Here is the topology file ;virtual sites have zero mass which leads to zero Moment of inertia ;virual sites have charge only 0.482 e. to balance the nitrogen atom negative charge -0.482 e. ;the distance between two nitrogn atoms is 0.11 nm ;the distance between two virtual sites is 0.15 nm ;the distance between nitrogen atom and virtual site is 0.02 nm. This makes the virtual site attached to the nitrogen atom [ atomtypes ] ;name bond_type mass charge ptypesigma epsilon N N 0.000 0.000 A 0.332 0.3026 MM0.000 0.000 V 0.000 0.000 ; [ moleculetype ] ; name nrexcl N_2 2 [ atoms ] ; nr typeresnr residue atom cgnrcharge mass typeBchargeB massB 1 N 1N_2 N1 1-0.48214.0067 2 N 1N_2 N2 1-0.48214.0067 3 M 1N_2 M1 1 0.4820. ; MN is the virtual site 4 M 1N_2 M2 1 0.4820. [ constraints ] ; There are no bonds in this system ; Instead, we fix the distance between the mass centers such that ; the virtual sites can be reconstructed 1 2 1 0.11 [ system ] Nitrogen in vacuo [ molecules ] N_2 1000 - here is the pdb file TITLE N_2 with dummy masses REMARKTHIS IS A SIMULATION BOX CRYST1 50.000 50.000 50.000 90.00 90.00 90.00 P 1 1 MODEL1 ATOM 1 N1 N_2 1 0.000 0.000 0.000 1.00 0.00 ATOM 2 N2 N_2 1 1.100 0.000 0.000 1.00 0.00 ATOM 3 M1 N_2 1 0.200 0.000 0.000 1.00 0.00 ATOM 4 M2 N_2 1 0.900 0.000 0.000 1.00 0.00 TER ENDMDL --- Thank you On Tue, Jul 18, 2017 at 8:10 PM, Justin Lemkul wrote: On 7/17/17 3:39 PM, Ali Ahmed wrote: Dear Justin Here is the topology file I wrote. I included all the parameters rather than use a specific FF. Thank you for your support .. - ; virtual sites have zero mass which leads to zero Moment of inertia ;virual sites have charge only 0.482 e. to balance the nitrogen atom negative charge -0.482 e. ; the distance between two nitrogn atoms N--N is 0.11 nm ;the distance between two virtual sites is 0.15 nm ;the distance between nitrogen atom and virtual site is 0.02 nm. This makes the virtual site attached to the nitrogen atom ; [ atomtypes ] ; name bond_typemasscharge ptype sigma epsilon N N 0.000 0.000 A 0.332 0.3026 MN MN 0.000 0.000 A 0.000 0.000; MN is the virtual sites This is incorrect; the virtual site should be particle type V, not A. [ moleculetype ] ; name nrexcl N_2 2 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 N 1N_2 N1 1-0.482 14.0067 2 N 1N_2 N2 1-0.482 14.0067 3MN 1N_2 M11 0.482 0. 4MN 1N_2 M2 1 0.482 0. [ constraints ] ; There are no bonds in this system ; Instead, we fix the distance between the mass centers such that ; the virtual sites can be reconstructed 3 4 1 0.15 This is why your system is failing. You're defining a constraint between the virtual sites and no bonded interaction at all between the N atoms. If the N-N bond is to be constant at 0.11 nm, then set it as a constraint (between atoms 1 and 2) and construct the virtual sites based on the real atoms in the system. -Justin [ system ] CO2 in vacuo [ molecules ] N_2 30 On Mon, Jul 17, 2017 at 12:46 PM, Justin Lemkul wrote: On 7/17/17 12:31 PM, Ali Ahmed wrote: Dear Justin I have tried same what you have said. I followed the tutorial for CO2 but didn't work, gave an error during the energy minimization . I'm not sure what was the wrong, I noticed the N atoms (in the box) were separated from the virtual site after the error. If yo
Re: [gmx-users] nitrogen itp file with virtual site
Dear Justin I have checked and tried but still not working, it says ( invalid order for directive atomtypes). Please can you take a look on the following Here is the topology file ;virtual sites have zero mass which leads to zero Moment of inertia ;virual sites have charge only 0.482 e. to balance the nitrogen atom negative charge -0.482 e. ;the distance between two nitrogn atoms is 0.11 nm ;the distance between two virtual sites is 0.15 nm ;the distance between nitrogen atom and virtual site is 0.02 nm. This makes the virtual site attached to the nitrogen atom [ atomtypes ] ;name bond_type mass charge ptypesigma epsilon N N 0.000 0.000 A 0.332 0.3026 MM0.000 0.000 V 0.000 0.000 ; [ moleculetype ] ; name nrexcl N_2 2 [ atoms ] ; nr typeresnr residue atom cgnrcharge mass typeBchargeB massB 1 N 1N_2 N1 1-0.48214.0067 2 N 1N_2 N2 1-0.48214.0067 3 M 1N_2 M1 1 0.4820. ; MN is the virtual site 4 M 1N_2 M2 1 0.4820. [ constraints ] ; There are no bonds in this system ; Instead, we fix the distance between the mass centers such that ; the virtual sites can be reconstructed 1 2 1 0.11 [ system ] Nitrogen in vacuo [ molecules ] N_2 1000 - here is the pdb file TITLE N_2 with dummy masses REMARKTHIS IS A SIMULATION BOX CRYST1 50.000 50.000 50.000 90.00 90.00 90.00 P 1 1 MODEL1 ATOM 1 N1 N_2 1 0.000 0.000 0.000 1.00 0.00 ATOM 2 N2 N_2 1 1.100 0.000 0.000 1.00 0.00 ATOM 3 M1 N_2 1 0.200 0.000 0.000 1.00 0.00 ATOM 4 M2 N_2 1 0.900 0.000 0.000 1.00 0.00 TER ENDMDL --- Thank you On Tue, Jul 18, 2017 at 8:10 PM, Justin Lemkul wrote: > > > On 7/17/17 3:39 PM, Ali Ahmed wrote: > >> Dear Justin >> >> Here is the topology file I wrote. I included all the parameters rather >> than use a specific FF. >> >> Thank you for your support >> >> .. >> >> >> - >> >> ; virtual sites have zero mass which leads to zero Moment of inertia >> >> ;virual sites have charge only 0.482 e. to balance the nitrogen atom >> negative charge -0.482 e. >> >> ; the distance between two nitrogn atoms N--N is 0.11 nm >> >> ;the distance between two virtual sites is 0.15 nm >> >> ;the distance between nitrogen atom and virtual site is 0.02 nm. This >> makes >> the virtual site attached to the nitrogen atom >> >> ; >> >> [ atomtypes ] >> >> ; name bond_typemasscharge ptype sigma epsilon >> >> N N 0.000 0.000 A >> 0.332 0.3026 >> >>MN MN 0.000 0.000 A 0.000 >> 0.000; MN is the virtual sites >> >> > This is incorrect; the virtual site should be particle type V, not A. > > >> >> [ moleculetype ] >> >> ; name nrexcl >> >> N_2 2 >> >> >> >> [ atoms ] >> >> ; nr type resnr residue atom cgnr charge mass >> typeBchargeB massB >> >> 1 N 1N_2 N1 1-0.482 >> 14.0067 >> >> 2 N 1N_2 N2 1-0.482 >> 14.0067 >> >> 3MN 1N_2 M11 0.482 >> 0. >> >> 4MN 1N_2 M2 1 0.482 >> 0. >> >> >> >> [ constraints ] >> >> ; There are no bonds in this system >> >> ; Instead, we fix the distance between the mass centers such that >> >> ; the virtual sites can be reconstructed >> >> 3 4 1 0.15 >> >> > This is why your system is failing. You're defining a constraint between > the virtual sites and no bonded interaction at all between the N atoms. If > the N-N bond is to be constant at 0.11 nm, then set it as a constraint > (between atoms 1 and 2) and construct the virtual sites based on the real > atoms in the system. > > -Justin > > > [ system ] >> >> CO2 in vacuo >> >> >> >> [ molecules ] >> >> N_2 30 >> >> >> >> On Mon, Jul 17, 2017 at 12:46 PM, Justin Lemkul wrote: >> >> >>> >>> On 7/17/17 12:31 PM, Ali Ahmed wrote: >>> >>> Dear Justin I have tried same what you have said. I followed the tutorial for CO2 but didn't work, gave an error during the energy minimization . I'm not sure what was the wrong, I noticed the N atoms (in the box) were separated from the virtual site after the error. If you have
