[gmx-users] How to define (or modify) a new potential function in Gromacs?
Dear Gromacs community, I am attemping to use Gromacs for a Coarse - grained simulation. In our model, we have a term similar to the angle harmonic potential term, but the variable is not angle but the volume created by three consecutive vectors. I don't know if there is a way to implement that kind of potential in Gromacs? I am looking forward to hearing from you. Thank you very much in advanced, Best regards, *Lan Hoa* -- 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] ATOMTYPES directive
Dear Gromacs community, In the [ atomtypes ] directive, according to Gromacs manual, it should have 7 seperated fields, which are name, at.num, mass, charge, ptype, c6, c12. However, when I remove the field of at.num, Gromacs still works without notifying any error. If I insert 2 fields more, it still doesn't notify error. Only when I insert 3 fields more, it start notifying error. I don't understand how Gromacs read through all the parameters and determine what is c6, c12, etc... I am looking forward to hearing from you. Thank you very much in advance. Best regards, *Lan Hoa* -- 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] Exclusion - determine neighboring atoms by atom indices or by bond connections?
Dear Gromacs community, In the Gromacs manual, if nrexcl = 3, that means atoms i+1, i+2, i+3 are excluded from non-bonded interactions with atom i. I don't know how Gromacs determine the neighboring atoms, based on atom indices or bond connections? For example, if I have a simple connection between CA and CB atoms like the following CA(1) -CA(3)---CA(5)CA(7) | | | | CB(2) CB(4)CB(6) CB(8) Indices of atoms are shown in the brackets. If the neighbouring atoms are determined based on atom indices, that means CB(2) will not form non-bonded interactions with CA(3), CB(4),CA(5) but still form non-bonded interactions with CA(1), that is what I don't want since CB(2) and CA(1) already form bonded interaction (harmonic bond energy) It really confused me. I am looking forward to hearing from you. Thank you very much in advance. Best regards, *Lan Hoa* -- 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] Exchange temperature instead of exchange coordinate in replica exchange molecular dynamics?
Hi all, I am reading the paper "Replica-exchange molecular dynamics method for protein folding" by Yuko Okamoto. In this paper, they exchange temperatures of 2 replica. To evaluate that replica exchange is successful, they calculate exchange probability; plot the temperature, potential energy per replica versue time. In Gromacs, coordinates of replica are exchanged instead. So besides evaluating exchange probability, how do I know that the replica exchange is sucessful? Since we exchange coordinate, one replica just stay at 1 temperature, so we will not see the result of the paper by Yuko, I mean, one replica actually visit all the temperature. How about potential energy, should I expect that one replica visit all range of potential energy when we exchange coordinates of replica? Also, is this bad if exchange probability too high, let's say 0.8? Thanks in advance. Best regards, *Lan Hoa* -- 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] Dihedral angle parameters in Gromacs and Amber
*Dear Gromacs society,* *I don't know how Gromacs define and calculate the multiplicity and equilibrium dihedral angle? For example, in Amber, the multiplicity is 1 and -3 but in Gromacs it is 1 and 3; All phi0 values in gromacs are positive but they are negative in Amber.* *Thank you very much in advance.* *Best regards,* *Lan Hoa* -- 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] Space between the columns in the topology file of Gromacs
Thank you, Best, *Lan Hoa* 2017-06-15 17:02 GMT-05:00 Mark Abraham <mark.j.abra...@gmail.com>: > Hi, > > Those are simply fields separated by whitespace. Columns not relevant. > > Mark > > On Thu, 15 Jun 2017 22:10 lan hoa Trinh <trinhlan...@gmail.com> wrote: > > > Dear Gromacs society, > > I wonder if there is the default for the space between the columns in the > > topology file, for example: > > [ bonds ] > > ;ai aj funcr0(nm) Kb > > 12 1 3.805916447e-01 2.0e+04 > > 23 1 3.788218579e-01 2.0e+04 > > 34 1 3.790369375e-01 2.0e+04 > > > > Should it be fixed that ai, aj at the fix positions, i.e. 8 spaces of > tab > > size for example? > > I am looking forward to hearing from you. > > Best regards, > > *Lan Hoa* > > -- > > 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] Space between the columns in the topology file of Gromacs
Dear Gromacs society, I wonder if there is the default for the space between the columns in the topology file, for example: [ bonds ] ;ai aj funcr0(nm) Kb 12 1 3.805916447e-01 2.0e+04 23 1 3.788218579e-01 2.0e+04 34 1 3.790369375e-01 2.0e+04 Should it be fixed that ai, aj at the fix positions, i.e. 8 spaces of tab size for example? I am looking forward to hearing from you. Best regards, *Lan Hoa* -- 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] Topology file and itp file
awesome :) Thank you! *Lan Hoa* 2017-04-23 20:15 GMT-05:00 Justin Lemkul <jalem...@vt.edu>: > > > On 4/22/17 10:39 PM, lan hoa Trinh wrote: > >> Dear Justin, >> I am assessing based on a time series. You are right :), even I used the >> same topology file, the change over time of the potential energy is still >> different. It is good to know ^&^ . All the information you provided are >> very helpful. Ok, let me try to express what I 've understood so far: >> When we assess a single point energy, if the two topology are the same, we >> will get the same value of energy at a single point (which could be the >> starting point or an arbitrary point of the trajectory). However, due to >> > > Correct. > > the non-producibility, even we get the same value of energy at each single >> point, it is not true when we try to simulate over a period of time and >> what we can trust is the the average value. >> > > Correct. > > -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] Topology file and itp file
Dear Justin, I am assessing based on a time series. You are right :), even I used the same topology file, the change over time of the potential energy is still different. It is good to know ^&^ . All the information you provided are very helpful. Ok, let me try to express what I 've understood so far: When we assess a single point energy, if the two topology are the same, we will get the same value of energy at a single point (which could be the starting point or an arbitrary point of the trajectory). However, due to the non-producibility, even we get the same value of energy at each single point, it is not true when we try to simulate over a period of time and what we can trust is the the average value. Hum, do I understand wrongly again, hixx. Best regards, *Lan Hoa* 2017-04-22 20:41 GMT-05:00 Justin Lemkul <jalem...@vt.edu>: > > > On 4/22/17 9:06 PM, lan hoa Trinh wrote: > >> Dear Justin, >> I don't understand what you meant by saying MD is chaotic. You mean about >> velocity? I know that when we generate velocity based on Boltzmann >> distribution, we have to generate random number. However, what we call >> random numbers is not actually "random" because they are obeying >> algorithm. >> I don't know if I understand correctly but if we start from an initial >> value, we generate a "seed", and then we have a "random" series of number. >> However next time, when we rerun the simulation, the same series will be >> created. >> >> > This is not really what I was referring to at all. > > http://www.gromacs.org/Documentation/Terminology/Reproducibility > > What is not clear from your posts is really how you're assessing "same" > vs. "different" - you mention potential energy but you do not say what you > did. A time series? A single point energy? An average of some sort? If > your two simulations are too short to be considered converged, you will > probably get a different value. Whether that value means anything is an > open question. In the limit of ergodicity, a simple system like yours > should easily produce the same ensemble-average properties. But if you're > just testing whether or not your two topologies are the same, the only test > you need to do is what I suggested, a single-point energy. Compare apples > to apples. Or atoms to atoms, as it were :) > > -Justin > > *Lan Hoa* >> >> >> 2017-04-21 7:21 GMT-05:00 Justin Lemkul <jalem...@vt.edu>: >> >> >>> >>> On 4/20/17 4:37 PM, lan hoa Trinh wrote: >>> >>> Dear Mark, >>>> I equilibrated my system in NVT, and then plot the potential energy. >>>> However the potential energy created with the two topology is not match. >>>> Thanks in advance, >>>> >>>> >>> MD is chaotic, and even identical topologies will yield different >>> results. If you want to test the equivalence of a topology, you should >>> evaluate a single-point energy of an identical configuration of atoms >>> with >>> the two topologies. That's the only meaningful test. >>> >>> http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy >>> >>> -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
Re: [gmx-users] Topology file and itp file
Dear Justin, I don't understand what you meant by saying MD is chaotic. You mean about velocity? I know that when we generate velocity based on Boltzmann distribution, we have to generate random number. However, what we call random numbers is not actually "random" because they are obeying algorithm. I don't know if I understand correctly but if we start from an initial value, we generate a "seed", and then we have a "random" series of number. However next time, when we rerun the simulation, the same series will be created. *Lan Hoa* 2017-04-21 7:21 GMT-05:00 Justin Lemkul <jalem...@vt.edu>: > > > On 4/20/17 4:37 PM, lan hoa Trinh wrote: > >> Dear Mark, >> I equilibrated my system in NVT, and then plot the potential energy. >> However the potential energy created with the two topology is not match. >> Thanks in advance, >> > > MD is chaotic, and even identical topologies will yield different > results. If you want to test the equivalence of a topology, you should > evaluate a single-point energy of an identical configuration of atoms with > the two topologies. That's the only meaningful test. > > http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy > > -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] Topology file and itp file
Dear Mark, I equilibrated my system in NVT, and then plot the potential energy. However the potential energy created with the two topology is not match. Thanks in advance, Best regards, *Lan Hoa* 2017-04-20 14:25 GMT-05:00 Mark Abraham <mark.j.abra...@gmail.com>: > Hi, > > How are you assessing "different?" > > Mark > > On Thu, 20 Apr 2017 21:13 lan hoa Trinh <trinhlan...@gmail.com> wrote: > > > Dear All, > > I am modelling a system of spherical beads (which I named as Fi) which > only > > repulsive each other. I would highly appreciate if some one can have a > look > > at the following topology which I created: > > (ficoll1.top) > > [ defaults ] > > ;nbfunc comb-rule gen-pairs > >1 1 no > > > > > > [ atomtypes ] > > ;name mass charge ptype c10 c12 > > Fi 6.0000.000 A0.000 14000 > > > > [ moleculetype ] > > ;name nrexcl > > Ficoll 0 > > > > [atoms] > > ;nr type resnr residue atom cgnr charge mass > > 1 Fi 1 Fi Fi 1 0.000 6.000 > > > > > > [ system ] > > ; name > > Ficoll > > > > [molecules] > > ; namenumber > > Ficoll 64 > > > > I also created another topology: > > (ficoll2.top) > > > > [ defaults ] > > ;nbfunc comb-rule gen-pairs > >1 1 no > > > > #include "fi.itp" > > > > [ system ] > > ; name > > Ficoll > > > > [molecules] > > ; namenumber > > Ficoll 64 > > > > where fi.itp is the following: > > [ atomtypes ] > > ;name mass charge ptype c10 c12 > > Fi 6.0000.000 A0.000 14000 > > > > [ moleculetype ] > > ;name nrexcl > > Ficoll 0 > > > > [atoms] > > ;nr type resnr residue atom cgnr charge mass > > 1 Fi 1 Fi Fi 1 0.000 6.000 > > > > I expected that the simulation with the 2 topology files should gave the > > same results but they gave the different results, > > > > I don't understand what is wrong here. > > Thank you very much in advance. > > Best regards, > > *Lan Hoa* > > -- > > 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] Topology file and itp file
Dear All, I am modelling a system of spherical beads (which I named as Fi) which only repulsive each other. I would highly appreciate if some one can have a look at the following topology which I created: (ficoll1.top) [ defaults ] ;nbfunc comb-rule gen-pairs 1 1 no [ atomtypes ] ;name mass charge ptype c10 c12 Fi 6.0000.000 A0.000 14000 [ moleculetype ] ;name nrexcl Ficoll 0 [atoms] ;nr type resnr residue atom cgnr charge mass 1 Fi 1 Fi Fi 1 0.000 6.000 [ system ] ; name Ficoll [molecules] ; namenumber Ficoll 64 I also created another topology: (ficoll2.top) [ defaults ] ;nbfunc comb-rule gen-pairs 1 1 no #include "fi.itp" [ system ] ; name Ficoll [molecules] ; namenumber Ficoll 64 where fi.itp is the following: [ atomtypes ] ;name mass charge ptype c10 c12 Fi 6.0000.000 A0.000 14000 [ moleculetype ] ;name nrexcl Ficoll 0 [atoms] ;nr type resnr residue atom cgnr charge mass 1 Fi 1 Fi Fi 1 0.000 6.000 I expected that the simulation with the 2 topology files should gave the same results but they gave the different results, I don't understand what is wrong here. Thank you very much in advance. Best regards, *Lan Hoa* -- 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] Generate non-bonded combinations
Dear Gromacs community, I am using Gromacs to simulate a C-alpha structure and have the following topology file (created by http://smog-server.org/). [ defaults ] ;nbfunc comb-rule gen-pairs 1 1 no [ atomtypes ] ;name mass charge ptype c10 c12 CA 1.0000.000 A0.000 0.167772160E-04 [ moleculetype ] ;name nrexcl Macromolecule 3 [ atoms ] ;nr type resnr residue atom cgnr charge mass 1 CA 1 ASN CA 1 0.000 1.000 2 CA 2 LEU CA 2 0.000 1.000 3 CA 3 LYS CA 3 0.000 1.000 4 CA 4 THR CA 4 0.000 1.000 [ pairs ] ; i j type and weights 2 25 1 0.198921701E+01 0.132925132E+01 2 27 1 0.582768432E+02 0.765215442E+02 2 45 1 0.865830453E+01 0.776440056E+01 3 7 1 0.143745898E+02 0.142660275E+02 3 8 1 0.458838723E+02 0.574355228E+02 ... As I understand, VDW parameter will only be generated by grompp for pairs of atoms which are defined in the directive [pairs]. When I use grompp, the notification is: Generated 1 of the 1 non-bonded parameter combinations. Based on the above topology ([pairs]) i expected there are more non-bonded combination generated. Can anyone help me to explain this? Also: [ atomtypes ] ;name mass charge ptype c10 c12 CA 1.0000.000 A0.000 0.167772160E-04 At first, I thought it meant that the pairs which were not defined in the directive [pairs] will be repulsive only, but they choose genpairs=no, so it looks like there is nothing to do with the lines?? Please help me! Thanks in advance. Best regards, *Lan Hoa * -- 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.
