[gmx-users] Virtual Sites
I am trying to add virtual sites to a simulation with no mass or charge, just to make tracking the center of mass of groups later easier later on. However, I keep getting the warning "The mass of a vsiten constructing atom is <= 0" when i run grompp. Here's the section of my .itp file where i have defined them: [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 1 CHX rtp CHX q 0.0 1 CLAL 1CHXCL1 1 -0.151 35.453 ; qtot -0.151 . . . . 63 CA 1CHXCZ2 63 0.083 12.011 ; qtot 0.144 64 CLAL 1CHXCL2 64 -0.144 35.453 ; qtot 0 65 MCH3 1CHX V1 65 0 0 ; 66 MCH3 1CHX V2 66 0 0 ; 67 MCH3 1CHX V3 67 0 0 ; 68 MCH3 1CHX V4 68 0 0 ; 69 MCH3 1CHX V5 69 0 0 ; 70 MCH3 1CHX V6 70 0 0 ; 71 MCH3 1CHX V7 71 0 0 ; 72 MCH3 1CHX V8 72 0 0 ; 73 MCH3 1CHX V9 73 0 0 ; 74 MCH3 1CHXV10 74 0 0 ; 75 MCH3 1CHXV11 75 0 0 ; 76 MCH3 1CHXV12 76 0 0 ; [virtual_sitesn] 65 2 8 9 10 11 66 2 2 3 6 7 67 2 1 4 5 12 13 68 2 14 15 16 17 18 69 2 19 20 21 22 23 70 2 24 25 26 27 28 29 30 31 32 71 2 33 34 35 36 37 38 39 40 41 72 2 49 50 51 52 53 73 2 44 45 46 47 48 74 2 42 43 54 57 58 75 2 55 56 59 60 76 2 61 62 63 64 Am I defining something wrong here? -- View this message in context: http://gromacs.5086.x6.nabble.com/Virtual-Sites-tp5012975.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] Virtual sites error
Trying to add hydrogen virtual sites to the model (using -vsites h option in pdb2gmx) results in a salvo of error messages when running grommp to create .tpr file after the solvation: ERROR 1 [file topol_DNA_chain_A2.itp, line 1033]: No default Constr. No Conn. types ERROR 2 [file topol_DNA_chain_A2.itp, line 1034]: No default Constr. No Conn. types This lines in constraints section in the .itp file refer to pairs of two MCH3 and one MC atoms, which should serve (the way I understand the situation) as replacement methyl group in thymine. There are several more pairs of same errors corresponding to different thymine methyl groups in the DNA strands. Here is the relevant sections of the itp file for the first two errors: [ constraints ] ; aiaj functc0c1 2 3 2 110 111 2 110 112 2 111 112 2 [ atoms ] 110 CM321 DT C5110 0.0025 12.01 ; qtot -2.867 111 MCH3321 DT MC71111 0 7.517 ; qtot -2.867 112 MCH3321 DT MC72111 0 7.517 ; qtot -2.867 -- 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] Virtual Sites
Hi, I haven't tried it but it should work if you set verlet-buffer-drift=-1 and set rlist manually. Roland On Mon, Dec 2, 2013 at 3:20 PM, Brad Van Oosten wrote: > I am trying to add virtual sites to a simulation with no mass or charge, > just > to make tracking the center of mass of groups later easier later on. > > However, I keep getting the warning "The mass of a vsiten constructing atom > is <= 0" when i run grompp. > > Here's the section of my .itp file where i have defined them: > > [ atoms ] > ; nr type resnr residue atom cgnr charge mass typeB > chargeB massB > ; residue 1 CHX rtp CHX q 0.0 > 1 CLAL 1CHXCL1 1 -0.151 35.453 ; > qtot > -0.151 > . > . > . > . > > 63 CA 1CHXCZ2 63 0.083 12.011 ; > qtot > 0.144 > 64 CLAL 1CHXCL2 64 -0.144 35.453 ; > qtot > 0 > 65 MCH3 1CHX V1 65 0 0 ; > 66 MCH3 1CHX V2 66 0 0 ; > 67 MCH3 1CHX V3 67 0 0 ; > 68 MCH3 1CHX V4 68 0 0 ; > 69 MCH3 1CHX V5 69 0 0 ; > 70 MCH3 1CHX V6 70 0 0 ; > 71 MCH3 1CHX V7 71 0 0 ; > 72 MCH3 1CHX V8 72 0 0 ; > 73 MCH3 1CHX V9 73 0 0 ; > 74 MCH3 1CHXV10 74 0 0 ; > 75 MCH3 1CHXV11 75 0 0 ; > 76 MCH3 1CHXV12 76 0 0 ; > > [virtual_sitesn] > 65 2 8 9 10 11 > 66 2 2 3 6 7 > 67 2 1 4 5 12 13 > 68 2 14 15 16 17 18 > 69 2 19 20 21 22 23 > 70 2 24 25 26 27 28 29 30 31 32 > 71 2 33 34 35 36 37 38 39 40 41 > 72 2 49 50 51 52 53 > 73 2 44 45 46 47 48 > 74 2 42 43 54 57 58 > 75 2 55 56 59 60 > 76 2 61 62 63 64 > > > Am I defining something wrong here? > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Virtual-Sites-tp5012975.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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. > > > > > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] Virtual sites error
Unfortunately, the parameters required for certain virtual sites in nucleic acids are not define in the force field files that are shipped with Gromacs. Erik Marklund, PhD Postdoctoral Research Fellow Fulford JRF, Somerville College Department of Chemistry Physical & Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ > On 7 Oct 2015, at 11:33, Timofey Tyugashev wrote: > > Trying to add hydrogen virtual sites to the model (using -vsites h option in > pdb2gmx) results in a salvo of error messages when running grommp to create > .tpr file after the solvation: > > ERROR 1 [file topol_DNA_chain_A2.itp, line 1033]: > No default Constr. No Conn. types > > > ERROR 2 [file topol_DNA_chain_A2.itp, line 1034]: > No default Constr. No Conn. types > > This lines in constraints section in the .itp file refer to pairs of two MCH3 > and one MC atoms, which should serve (the way I understand the situation) as > replacement methyl group in thymine. There are several more pairs of same > errors corresponding to different thymine methyl groups in the DNA strands. > > Here is the relevant sections of the itp file for the first two errors: > > [ constraints ] > ; aiaj functc0c1 >2 3 2 > 110 111 2 > 110 112 2 > 111 112 2 > > [ atoms ] > > 110 CM321 DT C5110 0.0025 12.01 ; qtot -2.867 > 111 MCH3321 DT MC71111 0 7.517 ; qtot -2.867 > 112 MCH3321 DT MC72111 0 7.517 ; qtot -2.867 > -- > 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] Virtual sites error
This looks very strange that from the whole assortment of the molecules in the force field only a humble methyl group in thymine lacks proper definition causes such an error. Even nucleotides which I added myself to the force field files don't produce any errors Is there any way to remedy this without significant hassle? What things are exactly lacking? -- Message: 4 Date: Thu, 8 Oct 2015 11:15:17 + From: Erik Marklund To: "gmx-us...@gromacs.org" Subject: Re: [gmx-users] Virtual sites error Message-ID: <89ae0bec-6d9f-49a0-83e2-5ad8d7734...@chem.ox.ac.uk> Content-Type: text/plain; charset="us-ascii" Unfortunately, the parameters required for certain virtual sites in nucleic acids are not define in the force field files that are shipped with Gromacs. Erik Marklund, PhD Postdoctoral Research Fellow Fulford JRF, Somerville College Department of Chemistry Physical & Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ On 7 Oct 2015, at 11:33, Timofey Tyugashev wrote: Trying to add hydrogen virtual sites to the model (using -vsites h option in pdb2gmx) results in a salvo of error messages when running grommp to create .tpr file after the solvation: ERROR 1 [file topol_DNA_chain_A2.itp, line 1033]: No default Constr. No Conn. types ERROR 2 [file topol_DNA_chain_A2.itp, line 1034]: No default Constr. No Conn. types This lines in constraints section in the .itp file refer to pairs of two MCH3 and one MC atoms, which should serve (the way I understand the situation) as replacement methyl group in thymine. There are several more pairs of same errors corresponding to different thymine methyl groups in the DNA strands. Here is the relevant sections of the itp file for the first two errors: [ constraints ] ; aiaj functc0c1 2 3 2 110 111 2 110 112 2 111 112 2 [ atoms ] 110 CM321 DT C5110 0.0025 12.01 ; qtot -2.867 111 MCH3321 DT MC71111 0 7.517 ; qtot -2.867 112 MCH3321 DT MC72111 0 7.517 ; qtot -2.867 -- 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] Virtual sites error
If memory serves me right, the atom type for the carbon in the thymine ring lacks default constraint lengths to the dummy masses. That combination of atom types are not used for aminoacids. You will need to calculate what constraint lengths yield the correct geometry for the CH3-group, which is quite doable. It is sometimes pointed out however, here and elsewhere, that no vsite parameters have been rigorously tested for nucleic acids, only for proteins (to my knowledge). Kind regards, Erik > On 9 Oct 2015, at 11:55, Timofey Tyugashev wrote: > > > This looks very strange that from the whole assortment of the molecules in > the force field only a humble methyl group in thymine lacks proper definition > causes such an error. > Even nucleotides which I added myself to the force field files don't produce > any errors > Is there any way to remedy this without significant hassle? What things are > exactly lacking? >> -- >> >> Message: 4 >> Date: Thu, 8 Oct 2015 11:15:17 + >> From: Erik Marklund >> To: "gmx-us...@gromacs.org" >> Subject: Re: [gmx-users] Virtual sites error >> Message-ID: <89ae0bec-6d9f-49a0-83e2-5ad8d7734...@chem.ox.ac.uk> >> Content-Type: text/plain; charset="us-ascii" >> >> Unfortunately, the parameters required for certain virtual sites in nucleic >> acids are not define in the force field files that are shipped with Gromacs. >> >> Erik Marklund, PhD >> Postdoctoral Research Fellow >> Fulford JRF, Somerville College >> >> Department of Chemistry >> Physical & Theoretical Chemistry Laboratory >> University of Oxford >> South Parks Road >> Oxford >> OX1 3QZ >> >>> On 7 Oct 2015, at 11:33, Timofey Tyugashev wrote: >>> >>> Trying to add hydrogen virtual sites to the model (using -vsites h option >>> in pdb2gmx) results in a salvo of error messages when running grommp to >>> create .tpr file after the solvation: >>> >>> ERROR 1 [file topol_DNA_chain_A2.itp, line 1033]: >>> No default Constr. No Conn. types >>> >>> >>> ERROR 2 [file topol_DNA_chain_A2.itp, line 1034]: >>> No default Constr. No Conn. types >>> >>> This lines in constraints section in the .itp file refer to pairs of two >>> MCH3 and one MC atoms, which should serve (the way I understand the >>> situation) as replacement methyl group in thymine. There are several more >>> pairs of same errors corresponding to different thymine methyl groups in >>> the DNA strands. >>> >>> Here is the relevant sections of the itp file for the first two errors: >>> >>> [ constraints ] >>> ; aiaj functc0c1 >>>2 3 2 >>> 110 111 2 >>> 110 112 2 >>> 111 112 2 >>> >>> [ atoms ] >>> >>> 110 CM321 DT C5110 0.0025 12.01 ; qtot >>> -2.867 >>> 111 MCH3321 DT MC71111 0 7.517 ; qtot >>> -2.867 >>> 112 MCH3321 DT MC72111 0 7.517 ; qtot >>> -2.867 >>> -- >>> 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] Virtual Sites + Capped Termini
Dear gmx users, I am trying to simulate a protein-ligand system in gromacs 5.1 with capped termini and using Virtual Sites. When I try to generate the tpr file with grompp, it seems that it is missing some constraint parameters for the bonds of C from ACE and N from NME with their respective virtual sites. The error I am receiving is the one that follows: *ERROR 1 [file topol.top, line 8967]:* * No default Constr. No Conn. types* *ERROR 2 [file topol.top, line 8968]:* * No default Constr. No Conn. types* *ERROR 3 [file topol.top, line 9505]:* * No default Constr. No Conn. types* *ERROR 4 [file topol.top, line 9506]:* * No default Constr. No Conn. types* where errors 1 and 2 correspond to ACE C-VS bonds and errors 3 and 4 correspond to NME N-VS bonds. Can you tell me what am I doing wrong? Thank you very much! *Joan Clark i Nicolas* -- 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] virtual sites for ligands?
Dear gmx-users, Is there a way to create a vsite-H topology of a ligand using gromacs (pdb2gmx)? Best regards, Carlos —— Carlos Navarro Retamal Bioinformatic Engineering. PhD. Postdoctoral Researcher in Center of Bioinformatics and Molecular Simulations Universidad de Talca Av. Lircay S/N, Talca, Chile E: carlos.navarr...@gmail.com or cnava...@utalca.cl -- 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] Virtual Sites + Capped Termini
On 10/22/15 9:05 AM, Joan Clark Nicolas wrote: Dear gmx users, I am trying to simulate a protein-ligand system in gromacs 5.1 with capped termini and using Virtual Sites. When I try to generate the tpr file with grompp, it seems that it is missing some constraint parameters for the bonds of C from ACE and N from NME with their respective virtual sites. The error I am receiving is the one that follows: *ERROR 1 [file topol.top, line 8967]:* * No default Constr. No Conn. types* *ERROR 2 [file topol.top, line 8968]:* * No default Constr. No Conn. types* *ERROR 3 [file topol.top, line 9505]:* * No default Constr. No Conn. types* *ERROR 4 [file topol.top, line 9506]:* * No default Constr. No Conn. types* where errors 1 and 2 correspond to ACE C-VS bonds and errors 3 and 4 correspond to NME N-VS bonds. Can you tell me what am I doing wrong? Probably nothing, but not all constraint types are necessarily defined, especially for capped termini. You will have to calculate appropriate [constrainttypes] for ffbonded.itp and add them. -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] Virtual Sites + Capped Termini
Hi again! I think I have solved the problem adding the following lines to the [ constrainttypes ] section of ffbonded.itp: ; constraints for capped termini MCH3 C 20.166426 MCH3 C 20.166426 N MCH320.166426 N MCH320.166426 where 0.166426 is the constraint parameter for rigid CH3 groups. Then I change the names of my Virtual Sites in the capped termini from MCH1 and MCH2 to MCH3 and it runs fine, but I am not sure that I am choosing the correct parameters, especially for the N-MCH3 bond. What do you think? Thanks! *Joan Clark i Nicolas* 2015-10-22 17:41 GMT+01:00 Justin Lemkul : > > > On 10/22/15 9:05 AM, Joan Clark Nicolas wrote: > >> Dear gmx users, >> >> I am trying to simulate a protein-ligand system in gromacs 5.1 with capped >> termini and using Virtual Sites. >> When I try to generate the tpr file with grompp, it seems that it is >> missing some constraint parameters for the bonds of C from ACE and N from >> NME with their respective virtual sites. The error I am receiving is the >> one that follows: >> >> >> *ERROR 1 [file topol.top, line 8967]:* >> * No default Constr. No Conn. types* >> >> >> *ERROR 2 [file topol.top, line 8968]:* >> * No default Constr. No Conn. types* >> >> >> *ERROR 3 [file topol.top, line 9505]:* >> * No default Constr. No Conn. types* >> >> >> *ERROR 4 [file topol.top, line 9506]:* >> * No default Constr. No Conn. types* >> >> where errors 1 and 2 correspond to ACE C-VS bonds and errors 3 and 4 >> correspond to NME N-VS bonds. Can you tell me what am I doing wrong? >> >> > Probably nothing, but not all constraint types are necessarily defined, > especially for capped termini. You will have to calculate appropriate > [constrainttypes] for ffbonded.itp and add them. > > -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.
[gmx-users] Virtual sites and diffusion coefficients.
Dear all, I tried simulating the CO2-water mixture with CO2 at a low concentration (0.003 mole fraction) at various temperatures at 1 atmos. I used the EPM2 parameters for the CO2 molecules which includes a flexible OCO angle. I did a separate simulation on the similar system with CO2 model constructed using virtual sites (following Justin Lemkul's tutorial) , with the interaction parameters same as the EPM2 model. In both cases the water model TIP4P was used. I ran 5ns simulation after equilibrium was attained for the T and P values. When plotting the mean square displacement and fitting the graph to get the diffusion coefficients, what I find is that the diffusion coefficient obtained in the case of the CO2 model using virtual sites is much higher (approximately two times) of that obtained for the EPM2 model without the virtual sites. Let me know if any one came across this before. I would like to hear from the more experienced users, what they think about this. I will provide further details on the topology and MD parameters if necessary. Regards, Sujith. -- 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] virtual sites for ligands?
Hi, No, you'll have to build such a topology yourself Mark On Fri., 12 Jul. 2019, 19:21 Carlos Navarro, wrote: > Dear gmx-users, > Is there a way to create a vsite-H topology of a ligand using gromacs > (pdb2gmx)? > Best regards, > Carlos > > —— > Carlos Navarro Retamal > Bioinformatic Engineering. PhD. > Postdoctoral Researcher in Center of Bioinformatics and Molecular > Simulations > Universidad de Talca > Av. Lircay S/N, Talca, Chile > E: carlos.navarr...@gmail.com or cnava...@utalca.cl > -- > 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] Virtual Sites in protein-ligand systems
Dear gmx users, I am trying to run MD calculations on a protein-ligand system using Virtual Sites, but as I generate my protein and ligand topologies separately (with pdb2gmx and acpype, respectively), the VS for the ligand are not generated. Does anyone know a way to generate the VS for the ligand without adding it to the force field? Thanks! *Joan Clark i Nicolas* -- 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] Virtual sites causing npt simulation instabilities
Hello all, I am having an issue with the current systems I am working on. The system consists of 2000 6point water molecules (3 chargeless masses for Ow, hw1, and hw2; and 3 massless point charges for the electrostatics). The three point charges I have implemented as virtual interaction sites using the section below in my topology file. [ virtual_sites3 ] ; Vsite fromfunct a b 4 1 2 3 1 0.29869481802 0.29869481802 ; Vsite (3fad) functtheta d 5 3 2 1 3 18.060.025 6 2 3 1 3 18.060.025 this is loosely based on the tip4p model. Since the two partial charges off of the hydrogens differ only in location I have them defined as a single type with sigma and epsilon defined as 0. I have also done this to the partial charge off of the oxygen. This is all seen below in my atomtypes and atoms sections. [ atomtypes ] ; name bond_typemasscharge ptype sigma epsilon qm1 qm1 0.000 -2.516A 0.000 0.000 qh1 qh1 0.0001.258A 0.000 0.000 --- [ atoms ] ; idat type res nr residu name at name cg nr charge 1 opls_1131 M3 OW 1 0.0 2 opls_1141 M3 HW1 1 0.0 3 opls_1141 M3 HW2 1 0.0 4 qm1 1 M3 qm 1 -2.516 5 qh1 1 M3 qh1 1 1.258 6 qh1 1 M3 qh2 1 1.258 The problem I am seeing right now depends on the parameters I use in the mdp files. During thermostat equlibration nothing is amiss, but once the volume of the box is allowed to relax the problems show. Using the parrinello-rahman barostat and 0.002fs timestep I crash with lincs warnings. Reducing the timestep to 0.001fs stops the lincs warnings, but the box size never converges It instead expands to around 10x its original size. So I think that I must have a problem with the implementation of my virtual sites. Any guidance would be greatly appreciated. Thanks below are some other parameters I have set in my input files. Andrew integrator = md nsteps = 50 nstcomm = 100 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstenergy = 1000 nstxtcout = 1000 nstlist = 5 ns_type = grid pbc = xyz coulombtype = pme rcoulomb= 0.5 rlist = 0.5 vdw-type= cut-off rvdw=0.5 constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 8 fourierspacing = 0.10 pme_order= 6 ewald_rtol = 1e-06 ewald_geometry = 3d optimize_fft = yes tcoupl = Nose-Hoover tc-grps = System tau_t = 0.4 ref_t = 300 ; Pressure coupling is on pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 2.0 ref_p = 1.0 compressibility = 4.5e-5 refcoord-scaling = com DispCorr= EnerPres comm-mode = linear -- 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] Virtual sites and diffusion coefficients.
Hi, With which set of parameters are you able to reproduce the original parametrization results? Mark On Tue, Feb 3, 2015 at 8:04 AM, sujithkakkat . wrote: > Dear all, > > I tried simulating the CO2-water mixture with CO2 at a low > concentration (0.003 mole fraction) at various temperatures at 1 atmos. > > I used the EPM2 parameters for the CO2 molecules which includes a flexible > OCO angle. I did a separate simulation on the similar system with CO2 model > constructed using virtual sites (following Justin Lemkul's tutorial) , with > the interaction parameters same as the EPM2 model. > > In both cases the water model TIP4P was used. > > I ran 5ns simulation after equilibrium was attained for the T and P values. > > When plotting the mean square displacement and fitting the graph to get > the diffusion coefficients, what I find is that the diffusion coefficient > obtained in the case of the CO2 model using virtual sites is much higher > (approximately two times) of that obtained for the EPM2 model without the > virtual sites. > > Let me know if any one came across this before. I would like to hear from > the more experienced users, what they think about this. > > I will provide further details on the topology and MD parameters if > necessary. > > Regards, > > Sujith. > -- > 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] Virtual sites and diffusion coefficients.
Hello Mark, I have tested both models in simulating a variety of properties. The original parametrization results involved predicting the critical point of CO2 and also density at various P and T. I did several NVT simulations to predict density-vs-pressure data. In this case the model with virtual interaction sites gave much better results. In addition to this, simulations performed were performed on pure CO2 at supercritical conditions and mean square displacement was calculated for the CO2 molecule. When compared to the reported ab initio dynamics results the one obtained using virtual sites gave much better agreement. The density of CO2 dissolved in H2O at very dilute concentrations was also studied using both models of CO2 and the results were in good agreement with experimental data for the model with virtual sites. In this case the one without virtual sites also did reasonably well. However, the disparity appears when considering the Measn Square displacement of dilute CO2 solution in water. Here the model without virtual sites is closer to the experimental data. This has become very confusing now. The original parametrization of he model did not involve predicting the transport properties. Also in the published results using the EPM2 model I don't find any mention of the virtual interaction sites. Regards, Sujith. On Tue, Feb 3, 2015 at 1:40 PM, Mark Abraham wrote: > Hi, > > With which set of parameters are you able to reproduce the original > parametrization results? > > Mark > > On Tue, Feb 3, 2015 at 8:04 AM, sujithkakkat . > wrote: > > > Dear all, > > > > I tried simulating the CO2-water mixture with CO2 at a low > > concentration (0.003 mole fraction) at various temperatures at 1 atmos. > > > > I used the EPM2 parameters for the CO2 molecules which includes a > flexible > > OCO angle. I did a separate simulation on the similar system with CO2 > model > > constructed using virtual sites (following Justin Lemkul's tutorial) , > with > > the interaction parameters same as the EPM2 model. > > > > In both cases the water model TIP4P was used. > > > > I ran 5ns simulation after equilibrium was attained for the T and P > values. > > > > When plotting the mean square displacement and fitting the graph to get > > the diffusion coefficients, what I find is that the diffusion coefficient > > obtained in the case of the CO2 model using virtual sites is much higher > > (approximately two times) of that obtained for the EPM2 model without the > > virtual sites. > > > > Let me know if any one came across this before. I would like to hear > from > > the more experienced users, what they think about this. > > > > I will provide further details on the topology and MD parameters if > > necessary. > > > > Regards, > > > > Sujith. > > -- > > 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] Virtual sites and diffusion coefficients.
On 2/3/15 3:56 AM, sujithkakkat . wrote: Hello Mark, I have tested both models in simulating a variety of properties. The original parametrization results involved predicting the critical point of CO2 and also density at various P and T. I did several NVT simulations to predict density-vs-pressure data. In this case the model with virtual interaction sites gave much better results. In addition to this, simulations performed were performed on pure CO2 at supercritical conditions and mean square displacement was calculated for the CO2 molecule. When compared to the reported ab initio dynamics results the one obtained using virtual sites gave much better agreement. The density of CO2 dissolved in H2O at very dilute concentrations was also studied using both models of CO2 and the results were in good agreement with experimental data for the model with virtual sites. In this case the one without virtual sites also did reasonably well. However, the disparity appears when considering the Measn Square displacement of dilute CO2 solution in water. Here the model without virtual sites is closer to the experimental data. This has become very confusing now. The original parametrization of he model did not involve predicting the transport properties. Also in the published results using the EPM2 model I don't find any mention of the virtual interaction sites. I'm rather amazed that my tutorial model works so well, but please note the strong caution I wrote in the topology. There is no validation of this model at all, anywhere in the literature. Any reviewer of your work is going to certainly want an explanation of the parameters, and "some model from a tutorial that says it isn't guaranteed to be physically valid" probably isn't going to satisfy them. -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.
[gmx-users] Virtual sites and diffusion coefficients for CO2
Dear all, I am using rigid CO2 model with virtual sites. The bond lengthe and LJ parameters are taken from TraPPE force field (Vapor–liquid equilibria of mixtures containing alkanes, carbon dioxide, and nitrogen. JJ Potoff, JI Siepmann. AIChE journal 47 (7), 1676-1682, 2001. 469). I followed Justin A. Lemkul's tutorial to construct the virtual sites (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/vsites/index.html). I find everything is OK except for the diffusion coeffients for CO2 are strange. The value with virtual sites (144.3087 (+/- 2.4934) 1e-5 cm^2/s) is half of that without virtual sites (282.5691 (+/- 20.2510) 1e-5 cm^2/s) . I just simulated 256 CO2 molecules at 298K and 55.2 bar with GROMACS 5.0.4. The itp files for CO2 with virtual sites is attched below. I found someone else also encounter such problems as shown in https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-February/095205.html and http://comments.gmane.org/gmane.science.biology.gromacs.user/23002 , and nobody solve out the origin of this issue. Could anybody help me to check the itp files I build and find out the origin of this issue. Thanks in advance! CO2_atomtypes.itp [ atomtypes ] ;name bond_typemasscharge ptype sigma epsilon OZOZ 15.99940 0.A 3.0500e-01 0.656806e0 CZCZ 12.01100 0.A 2.8000e-01 0.224478e0 MCO MCO 0.0000.000 A 0.000 0.000 CO2_rigid.itp [ moleculetype ] ; Name nrexcl CO2 2 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB 1 OZ 1CO2 O1 1 -0.350.00 2 CZ 1CO2 C 10.700.00 3 OZ 1CO2 O2 1 -0.35 0.00 4MCO 1CO2 M1 1 0.000 22.0049 5MCO 1CO2 M2 1 0.000 22.0049 [ constraints ] ; Overall structure is O1--M1---C---M2--O2 where "M" indicate mass centers ; There are no bonds in this system ; Instead, we fix the distance between the mass centers such that ; the virtual sites can be reconstructed 4 5 1 0.197995 [ virtual_sites2 ] ; the M1--O1 distance is 0.1161 - (0.197995/2) = 0.0171025 ; the M1--M2 distance is 0.197995 ; therefore, the fraction of the distance O1M2 along the M1--M2 length is (0.197995+0.0171025)/0.197995 = 1.0863784 ; thus placing the virtual O1 sites beyond the M1--M2 distance ; site ai(from) aj funct a 1 4 5 1 1.0863784 ; relative to mass center 4, extends beyond mass center 5 2 4 5 1 0.5000 ; right in the middle 3 5 4 1 1.0863784 ; as in the case of site 1 [ exclusions ] 1 2 3 2 1 3 3 1 2 itp files without Virtual sites CO2_atomtypes.itp [ atomtypes ] ;name bond_typemasscharge ptype sigma epsilon OZOZ 16. 0.A 3.0500e-01 0.656806e0 CZCZ 12. 0.A 2.8000e-01 0.224478e0 CO2_rigid.itp [ moleculetype ] ; Name nrexcl CO2 2 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB 1 OZ 1CO2 O1 1 -0.3516.00 2 CZ 1CO2 C 10.7012.00 3 OZ 1CO2 O2 1 -0.35 16.00 [ Constraints ] ; aiaj funct b0 1 2 1 0.1161 2 3 1 0.1161 1 3 1 0.2322 Best wishes! Zhongjin HE -- 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] Virtual Sites in protein-ligand systems
On 10/28/15 9:57 AM, Joan Clark Nicolas wrote: Dear gmx users, I am trying to run MD calculations on a protein-ligand system using Virtual Sites, but as I generate my protein and ligand topologies separately (with pdb2gmx and acpype, respectively), the VS for the ligand are not generated. Does anyone know a way to generate the VS for the ligand without adding it to the force field? One can define any [ virtual_sites* ] directive manually in the topology. pdb2gmx can build some types of virtual sites, but you'd have to tell us specifically what it is you're trying to do if you want anything really useful. Soon I will upload a patch that will make virtual site construction easier, and intrinsic to pdb2gmx. I just need to find the time to work out the kinks... -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] Virtual Sites in protein-ligand systems
I am trying to run MD calculations using a 5 fs timestep, so I need tu use Virtual Sites. The problem is that I generate ligand topology with acpype and then I add it to the protein topology, so the VS of the ligand are not generated. Maybe there is a way to generate VS for the ligand with acpype? And, about the [ virtual_sites* ] directive, can you tell me where can I read about this? maybe this is the thing I am looking for. Thank You! *Joan Clark i Nicolas* 2015-10-29 18:18 GMT+00:00 Justin Lemkul : > > > On 10/28/15 9:57 AM, Joan Clark Nicolas wrote: > >> Dear gmx users, >> I am trying to run MD calculations on a protein-ligand system using >> Virtual >> Sites, but as I generate my protein and ligand topologies separately (with >> pdb2gmx and acpype, respectively), the VS for the ligand are not >> generated. >> >> Does anyone know a way to generate the VS for the ligand without adding it >> to the force field? >> >> > One can define any [ virtual_sites* ] directive manually in the topology. > pdb2gmx can build some types of virtual sites, but you'd have to tell us > specifically what it is you're trying to do if you want anything really > useful. Soon I will upload a patch that will make virtual site > construction easier, and intrinsic to pdb2gmx. I just need to find the > time to work out the kinks... > > -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] Virtual Sites in protein-ligand systems
No, ACPYPE won’t give VS. But if I learn more about, I can try to implement. No guarantee though. On 30 October 2015 at 10:11, Joan Clark Nicolas wrote: > I am trying to run MD calculations using a 5 fs timestep, so I need tu use > Virtual Sites. The problem is that I generate ligand topology with acpype > and then I add it to the protein topology, so the VS of the ligand are not > generated. Maybe there is a way to generate VS for the ligand with acpype? > > And, about the [ virtual_sites* ] directive, can you tell me where can I > read about this? maybe this is the thing I am looking for. > > Thank You! > > > > *Joan Clark i Nicolas* > > 2015-10-29 18:18 GMT+00:00 Justin Lemkul : > > > > > > > On 10/28/15 9:57 AM, Joan Clark Nicolas wrote: > > > >> Dear gmx users, > >> I am trying to run MD calculations on a protein-ligand system using > >> Virtual > >> Sites, but as I generate my protein and ligand topologies separately > (with > >> pdb2gmx and acpype, respectively), the VS for the ligand are not > >> generated. > >> > >> Does anyone know a way to generate the VS for the ligand without adding > it > >> to the force field? > >> > >> > > One can define any [ virtual_sites* ] directive manually in the topology. > > pdb2gmx can build some types of virtual sites, but you'd have to tell us > > specifically what it is you're trying to do if you want anything really > > useful. Soon I will upload a patch that will make virtual site > > construction easier, and intrinsic to pdb2gmx. I just need to find the > > time to work out the kinks... > > > > -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. > -- Alan Wilter SOUSA da SILVA, DSc Senior Bioinformatician, UniProt European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Tel: +44 (0)1223 494588 -- 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] Virtual Sites in protein-ligand systems
On 10/30/15 6:11 AM, Joan Clark Nicolas wrote: I am trying to run MD calculations using a 5 fs timestep, so I need tu use Virtual Sites. The problem is that I generate ligand topology with acpype and then I add it to the protein topology, so the VS of the ligand are not generated. Maybe there is a way to generate VS for the ligand with acpype? At present, the simplest way forward is to take the information you have in your ligand topology from acpype and create an .rtp entry, then allow pdb2gmx to process the whole thing and build the virtual sites on the ligand. And, about the [ virtual_sites* ] directive, can you tell me where can I read about this? maybe this is the thing I am looking for. You can do this, but in addition to specifying the virtual sites (read in the PDF manual, it's all there), you will need to make the appropriate conversions in the [atoms] section and also build the coordinates for all virtual sites (e.g. the things that pdb2gmx does). -Justin Thank You! *Joan Clark i Nicolas* 2015-10-29 18:18 GMT+00:00 Justin Lemkul : On 10/28/15 9:57 AM, Joan Clark Nicolas wrote: Dear gmx users, I am trying to run MD calculations on a protein-ligand system using Virtual Sites, but as I generate my protein and ligand topologies separately (with pdb2gmx and acpype, respectively), the VS for the ligand are not generated. Does anyone know a way to generate the VS for the ligand without adding it to the force field? One can define any [ virtual_sites* ] directive manually in the topology. pdb2gmx can build some types of virtual sites, but you'd have to tell us specifically what it is you're trying to do if you want anything really useful. Soon I will upload a patch that will make virtual site construction easier, and intrinsic to pdb2gmx. I just need to find the time to work out the kinks... -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.
Re: [gmx-users] Virtual sites causing npt simulation instabilities
Always good practice to use Berendsen when turning on constant pressure first, it is much more robust than P-R. Let that run for awhile, let it equilibrate, then turn on P-R. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On 31 May 2018 at 06:40, Eisenhart, Andrew (eisenhaw) wrote: > Hello all, > > I am having an issue with the current systems I am working on. The system > consists of 2000 6point water molecules (3 chargeless masses for Ow, hw1, and > hw2; and 3 massless point charges for the electrostatics). The three point > charges I have implemented as virtual interaction sites using the section > below in my topology file. > > > [ virtual_sites3 ] > ; Vsite fromfunct a b > 4 1 2 3 1 0.29869481802 0.29869481802 > ; Vsite (3fad) functtheta d > 5 3 2 1 3 18.060.025 > 6 2 3 1 3 18.060.025 > > > this is loosely based on the tip4p model. Since the two partial charges off > of the hydrogens differ only in location I have them defined as a single type > with sigma and epsilon defined as 0. I have also done this to the partial > charge off of the oxygen. This is all seen below in my atomtypes and atoms > sections. > > > [ atomtypes ] > ; name bond_typemasscharge ptype sigma epsilon > qm1 qm1 0.000 -2.516A 0.000 0.000 > qh1 qh1 0.0001.258A 0.000 0.000 > > --- > > [ atoms ] > ; idat type res nr residu name at name cg nr charge > 1 opls_1131 M3 OW 1 0.0 > 2 opls_1141 M3 HW1 1 0.0 > 3 opls_1141 M3 HW2 1 0.0 > 4 qm1 1 M3 qm 1 -2.516 > 5 qh1 1 M3 qh1 1 1.258 > 6 qh1 1 M3 qh2 1 1.258 > > The problem I am seeing right now depends on the parameters I use in the mdp > files. During thermostat equlibration nothing is amiss, but once the volume > of the box is allowed to relax the problems show. Using the parrinello-rahman > barostat and 0.002fs timestep I crash with lincs warnings. Reducing the > timestep to 0.001fs stops the lincs warnings, but the box size never > converges It instead expands to around 10x its original size. So I think > that I must have a problem with the implementation of my virtual sites. Any > guidance would be greatly appreciated. Thanks below are some other parameters > I have set in my input files. > > Andrew > > > integrator = md > nsteps = 50 > nstcomm = 100 > nstxout = 0 > nstvout = 0 > nstfout = 0 > nstlog = 1000 > nstenergy = 1000 > nstxtcout = 1000 > nstlist = 5 > ns_type = grid > pbc = xyz > coulombtype = pme > rcoulomb= 0.5 > rlist = 0.5 > vdw-type= cut-off > rvdw=0.5 > constraint_algorithm = lincs > constraints = all-bonds > lincs_iter = 1 > lincs_order = 8 > fourierspacing = 0.10 > pme_order= 6 > ewald_rtol = 1e-06 > ewald_geometry = 3d > optimize_fft = yes > tcoupl = Nose-Hoover > tc-grps = System > tau_t = 0.4 > ref_t = 300 > ; Pressure coupling is on > pcoupl = parrinello-rahman > pcoupltype = isotropic > tau_p = 2.0 > ref_p = 1.0 > compressibility = 4.5e-5 > refcoord-scaling = com > DispCorr= EnerPres > comm-mode = linear > > > > -- > 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] Virtual sites causing npt simulation instabilities
On 5/30/18 4:40 PM, Eisenhart, Andrew (eisenhaw) wrote: Hello all, I am having an issue with the current systems I am working on. The system consists of 2000 6point water molecules (3 chargeless masses for Ow, hw1, and hw2; and 3 massless point charges for the electrostatics). The three point charges I have implemented as virtual interaction sites using the section below in my topology file. [ virtual_sites3 ] ; Vsite fromfunct a b 4 1 2 3 1 0.29869481802 0.29869481802 ; Vsite (3fad) functtheta d 5 3 2 1 3 18.060.025 6 2 3 1 3 18.060.025 this is loosely based on the tip4p model. Since the two partial charges off of the hydrogens differ only in location I have them defined as a single type with sigma and epsilon defined as 0. I have also done this to the partial charge off of the oxygen. This is all seen below in my atomtypes and atoms sections. [ atomtypes ] ; name bond_typemasscharge ptype sigma epsilon qm1 qm1 0.000 -2.516A 0.000 0.000 qh1 qh1 0.0001.258A 0.000 0.000 The particle type for these should be V. This could be the problem - if you've encoded an incorrect particle type then the update routines will not propagate them correctly. -Justin --- [ atoms ] ; idat type res nr residu name at name cg nr charge 1 opls_1131 M3 OW 1 0.0 2 opls_1141 M3 HW1 1 0.0 3 opls_1141 M3 HW2 1 0.0 4 qm1 1 M3 qm 1 -2.516 5 qh1 1 M3 qh1 1 1.258 6 qh1 1 M3 qh2 1 1.258 The problem I am seeing right now depends on the parameters I use in the mdp files. During thermostat equlibration nothing is amiss, but once the volume of the box is allowed to relax the problems show. Using the parrinello-rahman barostat and 0.002fs timestep I crash with lincs warnings. Reducing the timestep to 0.001fs stops the lincs warnings, but the box size never converges It instead expands to around 10x its original size. So I think that I must have a problem with the implementation of my virtual sites. Any guidance would be greatly appreciated. Thanks below are some other parameters I have set in my input files. Andrew integrator = md nsteps = 50 nstcomm = 100 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstenergy = 1000 nstxtcout = 1000 nstlist = 5 ns_type = grid pbc = xyz coulombtype = pme rcoulomb= 0.5 rlist = 0.5 vdw-type= cut-off rvdw=0.5 constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 8 fourierspacing = 0.10 pme_order= 6 ewald_rtol = 1e-06 ewald_geometry = 3d optimize_fft = yes tcoupl = Nose-Hoover tc-grps = System tau_t = 0.4 ref_t = 300 ; Pressure coupling is on pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 2.0 ref_p = 1.0 compressibility = 4.5e-5 refcoord-scaling = com DispCorr= EnerPres comm-mode = linear -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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] Virtual sites causing npt simulation instabilities
Hi, If that fixes the issue, then please let us know - we should consider fixing grompp to check that the inputs have appropriate consistency. Mark On Thu, May 31, 2018 at 1:48 PM Justin Lemkul wrote: > > > On 5/30/18 4:40 PM, Eisenhart, Andrew (eisenhaw) wrote: > > Hello all, > > > > I am having an issue with the current systems I am working on. The > system consists of 2000 6point water molecules (3 chargeless masses for Ow, > hw1, and hw2; and 3 massless point charges for the electrostatics). The > three point charges I have implemented as virtual interaction sites using > the section below in my topology file. > > > > > > [ virtual_sites3 ] > > ; Vsite fromfunct a b > > 4 1 2 3 1 0.29869481802 0.29869481802 > > ; Vsite (3fad) functtheta d > > 5 3 2 1 3 18.060.025 > > 6 2 3 1 3 18.060.025 > > > > > > this is loosely based on the tip4p model. Since the two partial charges > off of the hydrogens differ only in location I have them defined as a > single type with sigma and epsilon defined as 0. I have also done this to > the partial charge off of the oxygen. This is all seen below in my > atomtypes and atoms sections. > > > > > > [ atomtypes ] > > ; name bond_typemasscharge ptype sigma epsilon > >qm1 qm1 0.000 -2.516A 0.000 0.000 > >qh1 qh1 0.0001.258A 0.000 0.000 > > The particle type for these should be V. This could be the problem - if > you've encoded an incorrect particle type then the update routines will > not propagate them correctly. > > -Justin > > > --- > > > > [ atoms ] > > ; idat type res nr residu name at name cg nr charge > > 1 opls_1131 M3 OW 1 0.0 > > 2 opls_1141 M3 HW1 1 0.0 > > 3 opls_1141 M3 HW2 1 0.0 > > 4 qm1 1 M3 qm 1 -2.516 > > 5 qh1 1 M3 qh1 1 1.258 > > 6 qh1 1 M3 qh2 1 1.258 > > > > The problem I am seeing right now depends on the parameters I use in the > mdp files. During thermostat equlibration nothing is amiss, but once the > volume of the box is allowed to relax the problems show. Using the > parrinello-rahman barostat and 0.002fs timestep I crash with lincs > warnings. Reducing the timestep to 0.001fs stops the lincs warnings, but > the box size never converges It instead expands to around 10x its original > size. So I think that I must have a problem with the implementation of my > virtual sites. Any guidance would be greatly appreciated. Thanks below are > some other parameters I have set in my input files. > > > > Andrew > > > > > > integrator = md > > nsteps = 50 > > nstcomm = 100 > > nstxout = 0 > > nstvout = 0 > > nstfout = 0 > > nstlog = 1000 > > nstenergy = 1000 > > nstxtcout = 1000 > > nstlist = 5 > > ns_type = grid > > pbc = xyz > > coulombtype = pme > > rcoulomb= 0.5 > > rlist = 0.5 > > vdw-type= cut-off > > rvdw=0.5 > > constraint_algorithm = lincs > > constraints = all-bonds > > lincs_iter = 1 > > lincs_order = 8 > > fourierspacing = 0.10 > > pme_order= 6 > > ewald_rtol = 1e-06 > > ewald_geometry = 3d > > optimize_fft = yes > > tcoupl = Nose-Hoover > > tc-grps = System > > tau_t = 0.4 > > ref_t = 300 > > ; Pressure coupling is on > > pcoupl = parrinello-rahman > > pcoupltype = isotropic > > tau_p = 2.0 > > ref_p = 1.0 > > compressibility = 4.5e-5 > > refcoord-scaling = com > > DispCorr= EnerPres > > comm-mode = linear > > > > > > > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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/mai
Re: [gmx-users] Virtual sites causing npt simulation instabilities
Hey, Thanks for everyone's response. I have tried using the berendsen barostat, with it I see similar behavior with the unit cell jumping up in size and then steadily increasing in size. I have some longer runs using it running now (2-3ns), so I'll be able to see it it eventually converges. Nice catch with the particle type being incorrect, but with it corrected I'm still having the same problems (ie the oscillation of the box size) it has yet to throw lincs warnings though (even at ts = 2fs) so I'm going to simulate for a longer amount of time to see if it will converge. Thanks again for everyone's reply, below is my .itp in its entirety maybe there is an error in the exceptions(which im still not 100% sure about) or something else that will stand out. Andrew ; [ atomtypes ] ; name bond_typemasscharge ptype sigma epsilon qm1 qm1 0.000 -2.516V 0.000 0.000 qh1 qh1 0.0001.258V 0.000 0.000 [ moleculetype ] ; molname nrexcl M3 3 [ atoms ] ; idat type res nr residu name at name cg nr charge 1 opls_1131 M3 OW 1 0.0 2 opls_1141 M3 HW1 1 0.0 3 opls_1141 M3 HW2 1 0.0 4 qm1 1 M3 qm 1 -2.516 5 qh1 1 M3 qh1 1 1.258 6 qh1 1 M3 qh2 1 1.258 #ifndef FLEXIBLE [ settles ] ; OWfunct dohdhh 1 1 0.095720.15139 #else [ bonds ] ; i j funct length force.c. 1 2 1 0.09572 502416.0 0.09572502416.0 1 3 1 0.09572 502416.0 0.09572502416.0 [ angles ] ; i j k funct angle force.c. 2 1 3 1 104.52 628.02 104.52 628.02 #endif [ exclusions ] 1 2 3 4 5 6 2 1 3 4 5 6 3 1 2 4 5 6 4 1 2 3 5 6 5 1 2 3 4 6 6 1 2 3 4 5 [ virtual_sites3 ] ; Vsite fromfunct a b 4 1 2 3 1 0.29869481802 0.29869481802 ; Vsite (3fad) functtheta d 5 3 2 1 3 18.060.025 6 2 3 1 3 18.060.025 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham Sent: Thursday, May 31, 2018 7:54:09 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities Hi, If that fixes the issue, then please let us know - we should consider fixing grompp to check that the inputs have appropriate consistency. Mark On Thu, May 31, 2018 at 1:48 PM Justin Lemkul wrote: > > > On 5/30/18 4:40 PM, Eisenhart, Andrew (eisenhaw) wrote: > > Hello all, > > > > I am having an issue with the current systems I am working on. The > system consists of 2000 6point water molecules (3 chargeless masses for Ow, > hw1, and hw2; and 3 massless point charges for the electrostatics). The > three point charges I have implemented as virtual interaction sites using > the section below in my topology file. > > > > > > [ virtual_sites3 ] > > ; Vsite fromfunct a b > > 4 1 2 3 1 0.29869481802 0.29869481802 > > ; Vsite (3fad) functtheta d > > 5 3 2 1 3 18.060.025 > > 6 2 3 1 3 18.060.025 > > > > > > this is loosely based on the tip4p model. Since the two partial charges > off of the hydrogens differ only in location I have them defined as a > single type with sigma and epsilon defined as 0. I have also done this to > the partial charge off of the oxygen. This is all seen below in my > atomtypes and atoms sections. > > > > > > [ atomtypes ] > > ; name bond_typemasscharge ptype sigma epsilon > >qm1 qm1 0.000 -2.516A 0.000 0.000 > >qh1 qh1 0.0001.258A 0.000 0.000 > > The particle type for these should be V. This could be the problem - if > you've encoded an incorrect particle type then the update routines will > not propagate them correctly. > > -Justin > > > --- > > > > [ atoms ] > > ; idat type res nr residu name at name cg nr charge > > 1 opls_1131 M3 OW 1 0.0 > > 2 opls_1141 M3 HW1 1 0.0 > > 3 opls_1141 M3 HW2 1 0.0 > > 4 qm1 1 M3 qm 1 -2.516 > > 5 qh1 1 M3 qh1 1 1.258 > > 6 qh1 1 M3 qh2 1 1.258 > > > > The problem I am seeing right now depends on the parameters
Re: [gmx-users] Virtual sites causing npt simulation instabilities
Hello again, I have done a few things since I last updated this list. I generated a new system of only 1000 water instead of the original 2000, I used a more careful approach in my energy minimization, minimizing first with all bonds and angles constrained then again without those hash constraints. This succeeded in getting the maximum force in my system to below 100kcal without lincs warnings. Then I proceeded to equilibrate the temperature as before with no issues, and finally I attempted to equilibrate the box size using the Berendsen barostat running for 2ns. The box size increases as before and still does not converge. The system stays at around 300K, but after a while (~1ns) it seems to fill the box like its a gas visually at least. So any ideas that I could try would be appreciated. Thanks, Andrew From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Eisenhart, Andrew (eisenhaw) Sent: Thursday, May 31, 2018 1:51:51 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities Hey, Thanks for everyone's response. I have tried using the berendsen barostat, with it I see similar behavior with the unit cell jumping up in size and then steadily increasing in size. I have some longer runs using it running now (2-3ns), so I'll be able to see it it eventually converges. Nice catch with the particle type being incorrect, but with it corrected I'm still having the same problems (ie the oscillation of the box size) it has yet to throw lincs warnings though (even at ts = 2fs) so I'm going to simulate for a longer amount of time to see if it will converge. Thanks again for everyone's reply, below is my .itp in its entirety maybe there is an error in the exceptions(which im still not 100% sure about) or something else that will stand out. Andrew ; [ atomtypes ] ; name bond_typemasscharge ptype sigma epsilon qm1 qm1 0.000 -2.516V 0.000 0.000 qh1 qh1 0.0001.258V 0.000 0.000 [ moleculetype ] ; molname nrexcl M3 3 [ atoms ] ; idat type res nr residu name at name cg nr charge 1 opls_1131 M3 OW 1 0.0 2 opls_1141 M3 HW1 1 0.0 3 opls_1141 M3 HW2 1 0.0 4 qm1 1 M3 qm 1 -2.516 5 qh1 1 M3 qh1 1 1.258 6 qh1 1 M3 qh2 1 1.258 #ifndef FLEXIBLE [ settles ] ; OWfunct dohdhh 1 1 0.095720.15139 #else [ bonds ] ; i j funct length force.c. 1 2 1 0.09572 502416.0 0.09572502416.0 1 3 1 0.09572 502416.0 0.09572502416.0 [ angles ] ; i j k funct angle force.c. 2 1 3 1 104.52 628.02 104.52 628.02 #endif [ exclusions ] 1 2 3 4 5 6 2 1 3 4 5 6 3 1 2 4 5 6 4 1 2 3 5 6 5 1 2 3 4 6 6 1 2 3 4 5 [ virtual_sites3 ] ; Vsite fromfunct a b 4 1 2 3 1 0.29869481802 0.29869481802 ; Vsite (3fad) functtheta d 5 3 2 1 3 18.060.025 6 2 3 1 3 18.060.025 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham Sent: Thursday, May 31, 2018 7:54:09 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities Hi, If that fixes the issue, then please let us know - we should consider fixing grompp to check that the inputs have appropriate consistency. Mark On Thu, May 31, 2018 at 1:48 PM Justin Lemkul wrote: > > > On 5/30/18 4:40 PM, Eisenhart, Andrew (eisenhaw) wrote: > > Hello all, > > > > I am having an issue with the current systems I am working on. The > system consists of 2000 6point water molecules (3 chargeless masses for Ow, > hw1, and hw2; and 3 massless point charges for the electrostatics). The > three point charges I have implemented as virtual interaction sites using > the section below in my topology file. > > > > > > [ virtual_sites3 ] > > ; Vsite fromfunct a b > > 4 1 2 3 1 0.29869481802 0.29869481802 > > ; Vsite (3fad) functtheta d > > 5 3 2 1 3 18.060.025 > > 6 2 3 1 3 18.060.025 > > > > > > this is loosely based on the tip4p model. Since the two partial charges > off of the hydrogens differ only in location I have them defined as a > single type with sigma and epsilon defined as 0. I have also done this to > the partial charge off of the oxygen. This is all seen below in my > atomtypes and atoms sections. > > > > > > [ at
Re: [gmx-users] Virtual sites causing npt simulation instabilities
On 6/5/18 9:10 AM, Eisenhart, Andrew (eisenhaw) wrote: Hello again, I have done a few things since I last updated this list. I generated a new system of only 1000 water instead of the original 2000, I used a more careful approach in my energy minimization, minimizing first with all bonds and angles constrained then again without those hash constraints. This succeeded in getting the maximum force in my system to below 100kcal without lincs warnings. Then I proceeded to equilibrate the temperature as before with no issues, and finally I attempted to equilibrate the box size using the Berendsen barostat running for 2ns. The box size increases as before and still does not converge. The system stays at around 300K, but after a while (~1ns) it seems to fill the box like its a gas visually at least. So any ideas that I could try would be appreciated. If you can assemble a tarball that contains starting coordinates (not minimized), topology, all .mdp files, and a run script that gives the exact sequence of what you're doing, and post it somewhere to share, I will try to take a look at it and see if I can reproduce the behavior. What version of GROMACS are you using? -Justin Thanks, Andrew From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Eisenhart, Andrew (eisenhaw) Sent: Thursday, May 31, 2018 1:51:51 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities Hey, Thanks for everyone's response. I have tried using the berendsen barostat, with it I see similar behavior with the unit cell jumping up in size and then steadily increasing in size. I have some longer runs using it running now (2-3ns), so I'll be able to see it it eventually converges. Nice catch with the particle type being incorrect, but with it corrected I'm still having the same problems (ie the oscillation of the box size) it has yet to throw lincs warnings though (even at ts = 2fs) so I'm going to simulate for a longer amount of time to see if it will converge. Thanks again for everyone's reply, below is my .itp in its entirety maybe there is an error in the exceptions(which im still not 100% sure about) or something else that will stand out. Andrew ; [ atomtypes ] ; name bond_typemasscharge ptype sigma epsilon qm1 qm1 0.000 -2.516V 0.000 0.000 qh1 qh1 0.0001.258V 0.000 0.000 [ moleculetype ] ; molname nrexcl M3 3 [ atoms ] ; idat type res nr residu name at name cg nr charge 1 opls_1131 M3 OW 1 0.0 2 opls_1141 M3 HW1 1 0.0 3 opls_1141 M3 HW2 1 0.0 4 qm1 1 M3 qm 1 -2.516 5 qh1 1 M3 qh1 1 1.258 6 qh1 1 M3 qh2 1 1.258 #ifndef FLEXIBLE [ settles ] ; OWfunct dohdhh 1 1 0.095720.15139 #else [ bonds ] ; i j funct length force.c. 1 2 1 0.09572 502416.0 0.09572502416.0 1 3 1 0.09572 502416.0 0.09572502416.0 [ angles ] ; i j k funct angle force.c. 2 1 3 1 104.52 628.02 104.52 628.02 #endif [ exclusions ] 1 2 3 4 5 6 2 1 3 4 5 6 3 1 2 4 5 6 4 1 2 3 5 6 5 1 2 3 4 6 6 1 2 3 4 5 [ virtual_sites3 ] ; Vsite fromfunct a b 4 1 2 3 1 0.29869481802 0.29869481802 ; Vsite (3fad) functtheta d 5 3 2 1 3 18.060.025 6 2 3 1 3 18.060.025 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham Sent: Thursday, May 31, 2018 7:54:09 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities Hi, If that fixes the issue, then please let us know - we should consider fixing grompp to check that the inputs have appropriate consistency. Mark On Thu, May 31, 2018 at 1:48 PM Justin Lemkul wrote: On 5/30/18 4:40 PM, Eisenhart, Andrew (eisenhaw) wrote: Hello all, I am having an issue with the current systems I am working on. The system consists of 2000 6point water molecules (3 chargeless masses for Ow, hw1, and hw2; and 3 massless point charges for the electrostatics). The three point charges I have implemented as virtual interaction sites using the section below in my topology file. [ virtual_sites3 ] ; Vsite fromfunct a b 4 1 2 3 1 0.29869481802 0.29869481802 ; Vsite (3fad) functtheta d 5 3 2 1 3 18.060.025 6 2 3 1 3 18.060.025 this is loosely based on the tip4p model. Since the two partial charges off of the hydrogens differ only in location I have them defin
Re: [gmx-users] Virtual sites causing npt simulation instabilities
Here's the link to the files, if there's anything else I can send let me know. I've been using 5.1.1 for the initial set up and energy minimization, and 5.1.2 for the nvt and npt simulations. <https://files.fm/u/c9uef9qh> https://files.fm/u/c9uef9qh Thanks Andrew From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: Tuesday, June 5, 2018 12:54:50 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities On 6/5/18 9:10 AM, Eisenhart, Andrew (eisenhaw) wrote: > Hello again, > > I have done a few things since I last updated this list. > > > I generated a new system of only 1000 water instead of the original 2000, I > used a more careful approach in my energy minimization, minimizing first with > all bonds and angles constrained then again without those hash constraints. > This succeeded in getting the maximum force in my system to below 100kcal > without lincs warnings. > > > Then I proceeded to equilibrate the temperature as before with no issues, and > finally I attempted to equilibrate the box size using the Berendsen barostat > running for 2ns. The box size increases as before and still does not > converge. The system stays at around 300K, but after a while (~1ns) it seems > to fill the box like its a gas visually at least. > > So any ideas that I could try would be appreciated. If you can assemble a tarball that contains starting coordinates (not minimized), topology, all .mdp files, and a run script that gives the exact sequence of what you're doing, and post it somewhere to share, I will try to take a look at it and see if I can reproduce the behavior. What version of GROMACS are you using? -Justin > Thanks, > > Andrew > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Eisenhart, > Andrew (eisenhaw) > Sent: Thursday, May 31, 2018 1:51:51 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities > > Hey, > > Thanks for everyone's response. > > > I have tried using the berendsen barostat, with it I see similar behavior > with the unit cell jumping up in size and then steadily increasing in size. I > have some longer runs using it running now (2-3ns), so I'll be able to see it > it eventually converges. > > > Nice catch with the particle type being incorrect, but with it corrected I'm > still having the same problems (ie the oscillation of the box size) it has > yet to throw lincs warnings though (even at ts = 2fs) so I'm going to > simulate for a longer amount of time to see if it will converge. > > > Thanks again for everyone's reply, below is my .itp in its entirety maybe > there is an error in the exceptions(which im still not 100% sure about) or > something else that will stand out. > > > Andrew > > > ; > > [ atomtypes ] > ; name bond_typemasscharge ptype sigma epsilon >qm1 qm1 0.000 -2.516V 0.000 0.000 >qh1 qh1 0.0001.258V 0.000 0.000 > > [ moleculetype ] > ; molname nrexcl > M3 3 > > [ atoms ] > ; idat type res nr residu name at name cg nr charge > 1 opls_1131 M3 OW 1 0.0 > 2 opls_1141 M3 HW1 1 0.0 > 3 opls_1141 M3 HW2 1 0.0 > 4 qm1 1 M3 qm 1 -2.516 > 5 qh1 1 M3 qh1 1 1.258 > 6 qh1 1 M3 qh2 1 1.258 > #ifndef FLEXIBLE > > [ settles ] > ; OWfunct dohdhh > 1 1 0.095720.15139 > #else > [ bonds ] > ; i j funct length force.c. > 1 2 1 0.09572 502416.0 0.09572502416.0 > 1 3 1 0.09572 502416.0 0.09572502416.0 > > [ angles ] > ; i j k funct angle force.c. > 2 1 3 1 104.52 628.02 104.52 628.02 > #endif > > [ exclusions ] > 1 2 3 4 5 6 > 2 1 3 4 5 6 > 3 1 2 4 5 6 > 4 1 2 3 5 6 > 5 1 2 3 4 6 > 6 1 2 3 4 5 > > [ virtual_sites3 ] > ; Vsite fromfunct a b > 4 1 2 3 1 0.29869481802 0.29869481802 > ; Vsite (3fad) functtheta d > 5 3 2 1 3 18.060.025 > 6 2 3 1 3 18.060.025 > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Mark Abraham > > Sent: Thursday, May 31, 2018 7:54:
Re: [gmx-users] Virtual sites causing npt simulation instabilities
On 6/5/18 7:02 PM, Eisenhart, Andrew (eisenhaw) wrote: Here's the link to the files, if there's anything else I can send let me know. I've been using 5.1.1 for the initial set up and energy minimization, and 5.1.2 for the nvt and npt simulations. em.mdp is some corrupted binary file. Please upload a corrected version. -Justin <https://files.fm/u/c9uef9qh> https://files.fm/u/c9uef9qh Thanks Andrew From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: Tuesday, June 5, 2018 12:54:50 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities On 6/5/18 9:10 AM, Eisenhart, Andrew (eisenhaw) wrote: Hello again, I have done a few things since I last updated this list. I generated a new system of only 1000 water instead of the original 2000, I used a more careful approach in my energy minimization, minimizing first with all bonds and angles constrained then again without those hash constraints. This succeeded in getting the maximum force in my system to below 100kcal without lincs warnings. Then I proceeded to equilibrate the temperature as before with no issues, and finally I attempted to equilibrate the box size using the Berendsen barostat running for 2ns. The box size increases as before and still does not converge. The system stays at around 300K, but after a while (~1ns) it seems to fill the box like its a gas visually at least. So any ideas that I could try would be appreciated. If you can assemble a tarball that contains starting coordinates (not minimized), topology, all .mdp files, and a run script that gives the exact sequence of what you're doing, and post it somewhere to share, I will try to take a look at it and see if I can reproduce the behavior. What version of GROMACS are you using? -Justin Thanks, Andrew From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Eisenhart, Andrew (eisenhaw) Sent: Thursday, May 31, 2018 1:51:51 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities Hey, Thanks for everyone's response. I have tried using the berendsen barostat, with it I see similar behavior with the unit cell jumping up in size and then steadily increasing in size. I have some longer runs using it running now (2-3ns), so I'll be able to see it it eventually converges. Nice catch with the particle type being incorrect, but with it corrected I'm still having the same problems (ie the oscillation of the box size) it has yet to throw lincs warnings though (even at ts = 2fs) so I'm going to simulate for a longer amount of time to see if it will converge. Thanks again for everyone's reply, below is my .itp in its entirety maybe there is an error in the exceptions(which im still not 100% sure about) or something else that will stand out. Andrew ; [ atomtypes ] ; name bond_typemasscharge ptype sigma epsilon qm1 qm1 0.000 -2.516V 0.000 0.000 qh1 qh1 0.0001.258V 0.000 0.000 [ moleculetype ] ; molname nrexcl M3 3 [ atoms ] ; idat type res nr residu name at name cg nr charge 1 opls_1131 M3 OW 1 0.0 2 opls_1141 M3 HW1 1 0.0 3 opls_1141 M3 HW2 1 0.0 4 qm1 1 M3 qm 1 -2.516 5 qh1 1 M3 qh1 1 1.258 6 qh1 1 M3 qh2 1 1.258 #ifndef FLEXIBLE [ settles ] ; OWfunct dohdhh 1 1 0.095720.15139 #else [ bonds ] ; i j funct length force.c. 1 2 1 0.09572 502416.0 0.09572502416.0 1 3 1 0.09572 502416.0 0.09572502416.0 [ angles ] ; i j k funct angle force.c. 2 1 3 1 104.52 628.02 104.52 628.02 #endif [ exclusions ] 1 2 3 4 5 6 2 1 3 4 5 6 3 1 2 4 5 6 4 1 2 3 5 6 5 1 2 3 4 6 6 1 2 3 4 5 [ virtual_sites3 ] ; Vsite fromfunct a b 4 1 2 3 1 0.29869481802 0.29869481802 ; Vsite (3fad) functtheta d 5 3 2 1 3 18.060.025 6 2 3 1 3 18.060.025 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham Sent: Thursday, May 31, 2018 7:54:09 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities Hi, If that fixes the issue, then please let us know - we should consider fixing grompp to check that the inputs have appropriate consistency. Mark On Thu, May 31, 2018 at 1:48 PM Justin Lemkul wrote: On 5/30/18 4:40 PM, Eisenhart, Andrew (eisenhaw) wrote: Hello all,
Re: [gmx-users] Virtual sites causing npt simulation instabilities
Sorry about that, he’s a another link to the same files with the fixed em.mdp. I hope the 7zip format is ok. https://files.fm/u/r65e3kzq Andrew E. Eisenhart Graduate Research Assistant | University of Cincinnati 330.383.5061 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: Tuesday, June 5, 2018 7:05:51 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities On 6/5/18 7:02 PM, Eisenhart, Andrew (eisenhaw) wrote: > Here's the link to the files, if there's anything else I can send let me > know. I've been using 5.1.1 for the initial set up and energy minimization, > and 5.1.2 for the nvt and npt simulations. > em.mdp is some corrupted binary file. Please upload a corrected version. -Justin > <https://files.fm/u/c9uef9qh> > > https://files.fm/u/c9uef9qh > > > > Thanks > > Andrew > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Justin > Lemkul > Sent: Tuesday, June 5, 2018 12:54:50 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities > > > > On 6/5/18 9:10 AM, Eisenhart, Andrew (eisenhaw) wrote: >> Hello again, >> >> I have done a few things since I last updated this list. >> >> >> I generated a new system of only 1000 water instead of the original 2000, I >> used a more careful approach in my energy minimization, minimizing first >> with all bonds and angles constrained then again without those hash >> constraints. This succeeded in getting the maximum force in my system to >> below 100kcal without lincs warnings. >> >> >> Then I proceeded to equilibrate the temperature as before with no issues, >> and finally I attempted to equilibrate the box size using the Berendsen >> barostat running for 2ns. The box size increases as before and still does >> not converge. The system stays at around 300K, but after a while (~1ns) it >> seems to fill the box like its a gas visually at least. >> >> So any ideas that I could try would be appreciated. > If you can assemble a tarball that contains starting coordinates (not > minimized), topology, all .mdp files, and a run script that gives the > exact sequence of what you're doing, and post it somewhere to share, I > will try to take a look at it and see if I can reproduce the behavior. > > What version of GROMACS are you using? > > -Justin > >> Thanks, >> >> Andrew >> >> >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se >> on behalf of Eisenhart, >> Andrew (eisenhaw) >> Sent: Thursday, May 31, 2018 1:51:51 PM >> To: gmx-us...@gromacs.org >> Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities >> >> Hey, >> >> Thanks for everyone's response. >> >> >> I have tried using the berendsen barostat, with it I see similar behavior >> with the unit cell jumping up in size and then steadily increasing in size. >> I have some longer runs using it running now (2-3ns), so I'll be able to see >> it it eventually converges. >> >> >> Nice catch with the particle type being incorrect, but with it corrected I'm >> still having the same problems (ie the oscillation of the box size) it has >> yet to throw lincs warnings though (even at ts = 2fs) so I'm going to >> simulate for a longer amount of time to see if it will converge. >> >> >> Thanks again for everyone's reply, below is my .itp in its entirety maybe >> there is an error in the exceptions(which im still not 100% sure about) or >> something else that will stand out. >> >> >> Andrew >> >> >> ; >> >> [ atomtypes ] >> ; name bond_typemasscharge ptype sigma epsilon >> qm1 qm1 0.000 -2.516V 0.000 0.000 >> qh1 qh1 0.0001.258V 0.000 0.000 >> >> [ moleculetype ] >> ; molname nrexcl >> M3 3 >> >> [ atoms ] >> ; idat type res nr residu name at name cg nr charge >> 1 opls_1131 M3 OW 1 0.0 >> 2 opls_1141 M3 HW1 1 0.0 >> 3 opls_1141 M3 HW2 1 0.0 >> 4 qm1 1 M3 qm 1 -2.516 >> 5 qh1 1 M3 qh1 1 1.258 >> 6 qh1
Re: [gmx-users] Virtual sites causing npt simulation instabilities
On 6/5/18 9:28 PM, Eisenhart, Andrew (eisenhaw) wrote: Sorry about that, he’s a another link to the same files with the fixed em.mdp. I hope the 7zip format is ok. Please use tgz or just upload a plain-text em.mdp. -Justin https://files.fm/u/r65e3kzq Andrew E. Eisenhart Graduate Research Assistant | University of Cincinnati 330.383.5061 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: Tuesday, June 5, 2018 7:05:51 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities On 6/5/18 7:02 PM, Eisenhart, Andrew (eisenhaw) wrote: Here's the link to the files, if there's anything else I can send let me know. I've been using 5.1.1 for the initial set up and energy minimization, and 5.1.2 for the nvt and npt simulations. em.mdp is some corrupted binary file. Please upload a corrected version. -Justin <https://files.fm/u/c9uef9qh> https://files.fm/u/c9uef9qh Thanks Andrew From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: Tuesday, June 5, 2018 12:54:50 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities On 6/5/18 9:10 AM, Eisenhart, Andrew (eisenhaw) wrote: Hello again, I have done a few things since I last updated this list. I generated a new system of only 1000 water instead of the original 2000, I used a more careful approach in my energy minimization, minimizing first with all bonds and angles constrained then again without those hash constraints. This succeeded in getting the maximum force in my system to below 100kcal without lincs warnings. Then I proceeded to equilibrate the temperature as before with no issues, and finally I attempted to equilibrate the box size using the Berendsen barostat running for 2ns. The box size increases as before and still does not converge. The system stays at around 300K, but after a while (~1ns) it seems to fill the box like its a gas visually at least. So any ideas that I could try would be appreciated. If you can assemble a tarball that contains starting coordinates (not minimized), topology, all .mdp files, and a run script that gives the exact sequence of what you're doing, and post it somewhere to share, I will try to take a look at it and see if I can reproduce the behavior. What version of GROMACS are you using? -Justin Thanks, Andrew From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Eisenhart, Andrew (eisenhaw) Sent: Thursday, May 31, 2018 1:51:51 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities Hey, Thanks for everyone's response. I have tried using the berendsen barostat, with it I see similar behavior with the unit cell jumping up in size and then steadily increasing in size. I have some longer runs using it running now (2-3ns), so I'll be able to see it it eventually converges. Nice catch with the particle type being incorrect, but with it corrected I'm still having the same problems (ie the oscillation of the box size) it has yet to throw lincs warnings though (even at ts = 2fs) so I'm going to simulate for a longer amount of time to see if it will converge. Thanks again for everyone's reply, below is my .itp in its entirety maybe there is an error in the exceptions(which im still not 100% sure about) or something else that will stand out. Andrew ; [ atomtypes ] ; name bond_typemasscharge ptype sigma epsilon qm1 qm1 0.000 -2.516V 0.000 0.000 qh1 qh1 0.0001.258V 0.000 0.000 [ moleculetype ] ; molname nrexcl M3 3 [ atoms ] ; idat type res nr residu name at name cg nr charge 1 opls_1131 M3 OW 1 0.0 2 opls_1141 M3 HW1 1 0.0 3 opls_1141 M3 HW2 1 0.0 4 qm1 1 M3 qm 1 -2.516 5 qh1 1 M3 qh1 1 1.258 6 qh1 1 M3 qh2 1 1.258 #ifndef FLEXIBLE [ settles ] ; OWfunct dohdhh 1 1 0.095720.15139 #else [ bonds ] ; i j funct length force.c. 1 2 1 0.09572 502416.0 0.09572502416.0 1 3 1 0.09572 502416.0 0.09572502416.0 [ angles ] ; i j k funct angle force.c. 2 1 3 1 104.52 628.02 104.52 628.02 #endif [ exclusions ] 1 2 3 4 5 6 2 1 3 4 5 6 3 1 2 4 5 6 4 1 2 3 5 6 5 1 2 3 4 6 6 1 2 3 4 5 [ virtual_sites3 ] ; Vsite fromfunct a b 4 1 2 3 1 0.29869481802 0.29869481802 ; Vsite (3fad) functtheta d
Re: [gmx-users] Virtual sites causing npt simulation instabilities
new link with sole mdp file https://files.fm/u/cmyg863c From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: Tuesday, June 5, 2018 9:30 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities On 6/5/18 9:28 PM, Eisenhart, Andrew (eisenhaw) wrote: > Sorry about that, he’s a another link to the same files with the fixed > em.mdp. I hope the 7zip format is ok. Please use tgz or just upload a plain-text em.mdp. -Justin > https://files.fm/u/r65e3kzq [https://files.fm/images/files.fm-fb.png]<https://files.fm/u/r65e3kzq> 2018-06-06_r65e3kzq<https://files.fm/u/r65e3kzq> files.fm Fast, Secure and Easy cloud file hosting, storage and safe sharing. FTP alternative. Free signup. Unlimited download traffic via torrents. > > Andrew E. Eisenhart > Graduate Research Assistant | University of Cincinnati > 330.383.5061 > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Justin > Lemkul > Sent: Tuesday, June 5, 2018 7:05:51 PM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities > > > > On 6/5/18 7:02 PM, Eisenhart, Andrew (eisenhaw) wrote: >> Here's the link to the files, if there's anything else I can send let me >> know. I've been using 5.1.1 for the initial set up and energy minimization, >> and 5.1.2 for the nvt and npt simulations. >> > em.mdp is some corrupted binary file. Please upload a corrected version. > > -Justin > >> <https://files.fm/u/c9uef9qh> >> >> https://files.fm/u/c9uef9qh >> >> >> >> Thanks >> >> Andrew >> >> ____ >> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se >> on behalf of Justin >> Lemkul >> Sent: Tuesday, June 5, 2018 12:54:50 PM >> To: gmx-us...@gromacs.org >> Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities >> >> >> >> On 6/5/18 9:10 AM, Eisenhart, Andrew (eisenhaw) wrote: >>> Hello again, >>> >>> I have done a few things since I last updated this list. >>> >>> >>> I generated a new system of only 1000 water instead of the original 2000, I >>> used a more careful approach in my energy minimization, minimizing first >>> with all bonds and angles constrained then again without those hash >>> constraints. This succeeded in getting the maximum force in my system to >>> below 100kcal without lincs warnings. >>> >>> >>> Then I proceeded to equilibrate the temperature as before with no issues, >>> and finally I attempted to equilibrate the box size using the Berendsen >>> barostat running for 2ns. The box size increases as before and still does >>> not converge. The system stays at around 300K, but after a while (~1ns) it >>> seems to fill the box like its a gas visually at least. >>> >>> So any ideas that I could try would be appreciated. >> If you can assemble a tarball that contains starting coordinates (not >> minimized), topology, all .mdp files, and a run script that gives the >> exact sequence of what you're doing, and post it somewhere to share, I >> will try to take a look at it and see if I can reproduce the behavior. >> >> What version of GROMACS are you using? >> >> -Justin >> >>> Thanks, >>> >>> Andrew >>> >>> >>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se >>> on behalf of Eisenhart, >>> Andrew (eisenhaw) >>> Sent: Thursday, May 31, 2018 1:51:51 PM >>> To: gmx-us...@gromacs.org >>> Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities >>> >>> Hey, >>> >>> Thanks for everyone's response. >>> >>> >>> I have tried using the berendsen barostat, with it I see similar behavior >>> with the unit cell jumping up in size and then steadily increasing in size. >>> I have some longer runs using it running now (2-3ns), so I'll be able to >>> see it it eventually converges. >>> >>> >>> Nice catch with the particle type being incorrect, but with it corrected >>> I'm still having the same problems (ie the oscillation of the box size) it >>> has yet to throw lincs warnings though (even at ts = 2fs) so I'm going to >>> simulate for a longer amount of time to see if it will conv
Re: [gmx-users] Virtual sites causing npt simulation instabilities
On 6/6/18 11:13 AM, Eisenhart, Andrew (eisenhaw) wrote: new link with sole mdp file https://files.fm/u/cmyg863c This system doesn't even survive energy minimization for me, suggesting that the topology is not stable. The machine I'm on uses GROMACS 2016.3. Please upgrade to at least that version, if not 2018.1, because 5.1.2 is not even the terminal version in that series. Your topology specifies a SETTLE geometry for an SPC-like water, which immediately leads to each of your waters (which have O-H distances of 0.181 nm and H-H of 0.286 nm) to shrink inward, also shifting your virtual sites. That minimization simply crashes. I changed the SETTLE geometry to agree with your initial geometry, and while the atomic sites are OK, the qh1 and qh2 virtual sites expand outward, and though EM finishes, the max force is on the order of 10^8. Check your virtual site construction, as this may be the source of the buildup in force. Use "nstxout = 1" in your em.mdp to see this happening more clearly. Your cutoffs are bizarrely short but don't seem to be a problem. Once you've sorted out your topology issues, make sure your physical model is sane with such tiny cutoffs. -Justin From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: Tuesday, June 5, 2018 9:30 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities On 6/5/18 9:28 PM, Eisenhart, Andrew (eisenhaw) wrote: Sorry about that, he’s a another link to the same files with the fixed em.mdp. I hope the 7zip format is ok. Please use tgz or just upload a plain-text em.mdp. -Justin https://files.fm/u/r65e3kzq [https://files.fm/images/files.fm-fb.png]<https://files.fm/u/r65e3kzq> 2018-06-06_r65e3kzq<https://files.fm/u/r65e3kzq> files.fm Fast, Secure and Easy cloud file hosting, storage and safe sharing. FTP alternative. Free signup. Unlimited download traffic via torrents. Andrew E. Eisenhart Graduate Research Assistant | University of Cincinnati 330.383.5061 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: Tuesday, June 5, 2018 7:05:51 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities On 6/5/18 7:02 PM, Eisenhart, Andrew (eisenhaw) wrote: Here's the link to the files, if there's anything else I can send let me know. I've been using 5.1.1 for the initial set up and energy minimization, and 5.1.2 for the nvt and npt simulations. em.mdp is some corrupted binary file. Please upload a corrected version. -Justin <https://files.fm/u/c9uef9qh> https://files.fm/u/c9uef9qh Thanks Andrew From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: Tuesday, June 5, 2018 12:54:50 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities On 6/5/18 9:10 AM, Eisenhart, Andrew (eisenhaw) wrote: Hello again, I have done a few things since I last updated this list. I generated a new system of only 1000 water instead of the original 2000, I used a more careful approach in my energy minimization, minimizing first with all bonds and angles constrained then again without those hash constraints. This succeeded in getting the maximum force in my system to below 100kcal without lincs warnings. Then I proceeded to equilibrate the temperature as before with no issues, and finally I attempted to equilibrate the box size using the Berendsen barostat running for 2ns. The box size increases as before and still does not converge. The system stays at around 300K, but after a while (~1ns) it seems to fill the box like its a gas visually at least. So any ideas that I could try would be appreciated. If you can assemble a tarball that contains starting coordinates (not minimized), topology, all .mdp files, and a run script that gives the exact sequence of what you're doing, and post it somewhere to share, I will try to take a look at it and see if I can reproduce the behavior. What version of GROMACS are you using? -Justin Thanks, Andrew From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Eisenhart, Andrew (eisenhaw) Sent: Thursday, May 31, 2018 1:51:51 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Virtual sites causing npt simulation instabilities Hey, Thanks for everyone's response. I have tried using the berendsen barostat, with it I see similar behavior with the unit cell jumping up in size and then steadily increasing in size. I have some longer runs using it running now (2-3ns), so I'll be able to see it it eventually converges. Nice catch with the particle type being incorrect, but with it corrected I'm