Re: [gmx-users] LINCS WARNING
Dear Justin, I am so thankful for you kindly reply. Now, I can solve this problem. Tuong Vy On Tue, Oct 6, 2015 at 11:49 PM, Justin Lemkul wrote: > > > On 10/6/15 3:26 AM, Vy Phan wrote: > >> Dear all gromacs Users! >> I want to run a simulation with the system protein-ligand (I have several >> ligands). >> With EM, nvt, npt step I put position restraint for the ligands and all >> thing was fine. After that, I run production simulation without position >> restraint of ligands. I saw the ligand move out of the initial position >> and >> simulation was stopped. >> >> Did the LINCS warning happen because this system is not stable ? >> > > Yes. > > How can I keep the continuous running simulation without the LINCS >> warnings? I want the ligands are free to move and find their binding >> sites. >> >> > Either your ligand topology is not stable or your run settings are not > sensible. Please see any of the million or so posts in the gmx-users > mailing list archive regarding similar or identical situations. > > -Justin > > This is the warnings: >> Too many LINCS warnings (1000) >> If you know what you are doing you can adjust the lincs warning threshold >> in your mdp file >> or set the environment variable GMX_MAXCONSTRWARN to -1, >> but normally it is better to fix the problem >> >> Thank you so much for any suggestions >> Tuong Vy >> >> > -- > == > > 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] LINCS WARNING
Dear all gromacs Users! I want to run a simulation with the system protein-ligand (I have several ligands). With EM, nvt, npt step I put position restraint for the ligands and all thing was fine. After that, I run production simulation without position restraint of ligands. I saw the ligand move out of the initial position and simulation was stopped. Did the LINCS warning happen because this system is not stable ? How can I keep the continuous running simulation without the LINCS warnings? I want the ligands are free to move and find their binding sites. This is the warnings: Too many LINCS warnings (1000) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem Thank you so much for any suggestions Tuong Vy -- 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] Optimize the cut-off distance and fourierspacing
Dear All gromacs Users, Could you please tell me the way to optimize the cut-off distance and fourierspacing on Gromacs 5.0.4 ? Thank you so much Phan Vy -- 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] generate angle restraint and dihedral angle restraint file
Thank you Justin ! Phan Vy On Tue, Sep 8, 2015 at 8:29 PM, Justin Lemkul wrote: > > > On 9/8/15 2:24 AM, Vy Phan wrote: > >> Dear Gromacs Users, >> >> Are there avaluable command line to generate the angle restraint and >> dihedral file automatically? >> >> > Nope. > > -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] generate angle restraint and dihedral angle restraint file
Dear Gromacs Users, Are there avaluable command line to generate the angle restraint and dihedral file automatically? Thank you so much Phan Vy -- 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] infinite force at the membrane lipid
Dear HTH and Gromacs Users, Thank you HTH, I used the DOPC membrane lipid pdb file and topology from the website http://mmkluster.fos.su.se/slipids/Downloads.html. I running energy minimization for protein in water and lipid in water. After that, I put the protein into the center of membrane lipid and use tcl script to remove all overlapping moleculas by this script. [atomselect 0 " resname DOPC and (same residue as resname DOPC and x >25 and x<110 and y > 20 and y < 115) and not (same residue as resname DOPC and within 1 of protein)"] writepdb DOPC.pdb [atomselect 0 " water and (same residue as water and x > 20 and x<115 and y > 15 and y < 120) and not (same residue as water and within 1 of protein)"] writepdb wat.pdb After that I combine protein, lipid and water to one system and run. I did not use inflate_gro or g_membed tools. The g_membed tools can not used in Gromacs 5 (I use Gromacs 5.0.4) Hope you can see my problems and help me more. If you think the way I insert the protein on the lipid is the problem. Please let me know. I usually do this way with NAMD. Best regards, Tuong Vy 2015-08-16 20:21 GMT+09:00 ABEL Stephane 175950 : > Hello, > > How did you construct your membrane, with CHARMM-GUI? What is the lipid? > From my experience, I have found that sometimes CHARMM-GUI does not provide > a good starting point for MD. So I would suggest you to : > > - center the lipids inside the box to have no lipids that cross the box > limit and/or increase a little bit the box size (x-y) and minimize your > system again. > > Moreover to insert you protein inside the membrane, did you try the > inflate_gro or g_membed tools ? > > Good luck > > HTH > > ------ > > Message: 1 > Date: Sun, 16 Aug 2015 10:51:42 +0900 > From: Vy Phan > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] infinite force at the membrane lipid > Message-ID: > u6...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Dear Dr Justin and Gromacs User, > > This is my commands for running energy minimization. > > define = -DPOSRES > integrator = cg > > nstcgsteep = 1000 > emtol = 100.0 > emstep = 0.01 > dt = 0.002 > ; Output control > nstxout = 50 > nstenergy = 50 > nstlog = 50 > > > nstlist = 1 > cutoff-scheme = Verlet > ns_type = grid > coulombtype = PME > rcoulomb= 1.2 > vdw-modifier= Potential-shift > rvdw= 1.2 > rvdw-switch = 1.0 > pbc = xyz > > > I hope you can give more recommendations. Removing lipids actually is not > an appropriate solution. > > Thank you so much > > Tuong Vy > > 2015-08-16 1:47 GMT+09:00 Justin Lemkul : > > > > > > > On 8/15/15 12:41 PM, Vy Phan wrote: > > > >> Dear All gromacs Users, > >> > >> I want to run the membrane protein simulation. I run the energy > >> minimization for membrane and protein separately. > >> After that I combine protein and lipid together and remove the > >> overlapping > >> molecules. > >> when I run energy minimization I got the error "inf at atom on lipid". I > >> remove the lipid which includes this atom. I got the error several time > >> and I repeat remove lipid. I see the "inf at atom on lipid" always > happens > >> on lipids which locate at the wall (at the boundary of unit cell). > >> > >> I successfully run one time when I remove lipids have error, another > was > >> failed. > >> > >> I wonder why the error "inf at atom on lipid" always happens on lipids > >> which locate at the wall. Maybe I did something wrong about periodic > >> boundary condition. > >> > >> Thank you for any thoughts. > >> > >> > > Without a list of your exact commands and what you've done to this point, > > it's impossible to diagnose. There's something fundamentally wrong with > > the coordinates, topology, or both. If the infinite force is just moving > > around, what you're observing is a symptom, not a cause, and removing > > lipids to try to make it go away is not an appropriate solution. > > > > -Justin > > > > -- > > == > > > > Justin A. Lemkul, Ph.D. > > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > > > Department of Pharm
Re: [gmx-users] infinite force at the membrane lipid
Dear Dr Justin and Gromacs User, This is my commands for running energy minimization. define = -DPOSRES integrator = cg nstcgsteep = 1000 emtol = 100.0 emstep = 0.01 dt = 0.002 ; Output control nstxout = 50 nstenergy = 50 nstlog = 50 nstlist = 1 cutoff-scheme = Verlet ns_type = grid coulombtype = PME rcoulomb= 1.2 vdw-modifier= Potential-shift rvdw= 1.2 rvdw-switch = 1.0 pbc = xyz I hope you can give more recommendations. Removing lipids actually is not an appropriate solution. Thank you so much Tuong Vy 2015-08-16 1:47 GMT+09:00 Justin Lemkul : > > > On 8/15/15 12:41 PM, Vy Phan wrote: > >> Dear All gromacs Users, >> >> I want to run the membrane protein simulation. I run the energy >> minimization for membrane and protein separately. >> After that I combine protein and lipid together and remove the >> overlapping >> molecules. >> when I run energy minimization I got the error "inf at atom on lipid". I >> remove the lipid which includes this atom. I got the error several time >> and I repeat remove lipid. I see the "inf at atom on lipid" always happens >> on lipids which locate at the wall (at the boundary of unit cell). >> >> I successfully run one time when I remove lipids have error, another was >> failed. >> >> I wonder why the error "inf at atom on lipid" always happens on lipids >> which locate at the wall. Maybe I did something wrong about periodic >> boundary condition. >> >> Thank you for any thoughts. >> >> > Without a list of your exact commands and what you've done to this point, > it's impossible to diagnose. There's something fundamentally wrong with > the coordinates, topology, or both. If the infinite force is just moving > around, what you're observing is a symptom, not a cause, and removing > lipids to try to make it go away is not an appropriate solution. > > -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] infinite force at the membrane lipid
Dear All gromacs Users, I want to run the membrane protein simulation. I run the energy minimization for membrane and protein separately. After that I combine protein and lipid together and remove the overlapping molecules. when I run energy minimization I got the error "inf at atom on lipid". I remove the lipid which includes this atom. I got the error several time and I repeat remove lipid. I see the "inf at atom on lipid" always happens on lipids which locate at the wall (at the boundary of unit cell). I successfully run one time when I remove lipids have error, another was failed. I wonder why the error "inf at atom on lipid" always happens on lipids which locate at the wall. Maybe I did something wrong about periodic boundary condition. Thank you for any thoughts. Best regards Tuong Vy -- 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] Charmm 36 parameter file for gromacs
Dear Dr. Justin I got your means and it is very helpful for me. Thank you so much :) Sincerely, Tuong Vy 2015-08-12 21:23 GMT+09:00 Justin Lemkul : > > > On 8/12/15 8:20 AM, Vy Phan wrote: > >> Dear Dr Justin and Gromacs User, >> As I mentioned in the previous email , I download the parameter from this >> website which was build for all-atom simulation ( >> http://mmkluster.fos.su.se/slipids/Downloads.html ). I attached the file >> > > The list does not accept attachments, not is it necessary. > > below . I have a confusion with Tielema's website. I use this for run >> membrane protein simulations and it work well, no errors like the topology >> which was embedded in charmm36 force field for with Gromacs format. >> >> > Previous success with a different force field has no bearing on future > success with a different model that uses a different convention (all-atom > vs. united-atom). > > I just want to ask why I got many error when I use the topology which was >> embedded in charmm36 force field for with Gromacs format? Some suggestion >> to me please. >> >> > As I said before, you have serious problems with whatever topology you > managed to generate. A charge of +888 on a 516-lipid DOPC (which is > neutral) is total nonsense, so you certainly have missing or incorrect > atoms that you've bypassed with pdb2gmx options or something else. > Whatever that topology has in it is certainly wrong and should not be used. > > -Justin > > > Dear Dr. Justin >> Thank you so much for your suggestion. I will try with CHARMM-GUI. >> >> Best regards, >> Tuong Vy >> >> 2015-08-12 21:19 GMT+09:00 Vy Phan : >> >> Dear Dr Justin and Gromacs User, >>> As I mentioned in the previous email , I download the parameter from this >>> website which was build for all-atom simulation ( >>> http://mmkluster.fos.su.se/slipids/Downloads.html ). I attached the file >>> below . I have a confusion with Tielema's website. I use this for run >>> membrane protein simulations and it work well, no errors like the >>> topology >>> which was embedded in charmm36 force field for with Gromacs format. >>> >>> I just want to ask why I got many error when I use the topology which was >>> embedded in charmm36 force field for with Gromacs format? Some suggestion >>> to me please. >>> >>> Dear Dr. Justin >>> Thank you so much for your suggestion. I will try with CHARMM-GUI. >>> >>> Best regards, >>> Tuong Vy >>> >>> 2015-08-12 20:32 GMT+09:00 Justin Lemkul : >>> >>> >>>> >>>> On 8/11/15 10:15 PM, Vy Phan wrote: >>>> >>>> Dear Dr. Justin and Gromacs User, >>>>> >>>>> Thank you so much for your helps. >>>>> >>>>> When I use charmm36 ff to generate the topology for lipid (DOPC). I got >>>>> many warning "Warning :Long bond " >>>>> And after get the topology, the total charge is very high (+888 e for >>>>> DOPC >>>>> bilayer have 516 molecular). When I used grompp to generate the .tpr >>>>> file, >>>>> I got the many error like this : >>>>> Error 3379 [file topol_Other_chain_D.itp, line 198252] >>>>>No defaut U-B types >>>>> ... >>>>> Error 2379 [file topol_Other_chain_D.itp, line 98252] >>>>> No default Proper Dih.type >>>>> >>>>> >>>>> What can I do to modified the topology to get the correct charge and >>>>> fix >>>>> the error ? >>>>> >>>>> I download dopc.itp from Tieleman's website. I run simulation and all >>>>> things look fine. People have experiences, please tell me the >>>>> difference >>>>> of this topology and the one on the charmm36 force field. >>>>> >>>>> >>>>> The files Tieleman provides are united-atom structures that may use a >>>> different naming convention. They won't have H atoms on the aliphatic >>>> groups and there is no .hdb entry for DOPC. The ridiculous net charge >>>> you >>>> got for DOPC (which is neutral!) should be an indicator that whatever >>>> topology you built is utter nonsense. There should also be no warnings >>>> about missing parameters, so this is further evidence that the topology >>>> is >>>> wrong and the "thing
Re: [gmx-users] Charmm 36 parameter file for gromacs
Dear Dr Justin and Gromacs User, As I mentioned in the previous email , I download the parameter from this website which was build for all-atom simulation ( http://mmkluster.fos.su.se/slipids/Downloads.html ). I attached the file below . I have a confusion with Tielema's website. I use this for run membrane protein simulations and it work well, no errors like the topology which was embedded in charmm36 force field for with Gromacs format. I just want to ask why I got many error when I use the topology which was embedded in charmm36 force field for with Gromacs format? Some suggestion to me please. Dear Dr. Justin Thank you so much for your suggestion. I will try with CHARMM-GUI. Best regards, Tuong Vy 2015-08-12 21:19 GMT+09:00 Vy Phan : > Dear Dr Justin and Gromacs User, > As I mentioned in the previous email , I download the parameter from this > website which was build for all-atom simulation ( > http://mmkluster.fos.su.se/slipids/Downloads.html ). I attached the file > below . I have a confusion with Tielema's website. I use this for run > membrane protein simulations and it work well, no errors like the topology > which was embedded in charmm36 force field for with Gromacs format. > > I just want to ask why I got many error when I use the topology which was > embedded in charmm36 force field for with Gromacs format? Some suggestion > to me please. > > Dear Dr. Justin > Thank you so much for your suggestion. I will try with CHARMM-GUI. > > Best regards, > Tuong Vy > > 2015-08-12 20:32 GMT+09:00 Justin Lemkul : > >> >> >> On 8/11/15 10:15 PM, Vy Phan wrote: >> >>> Dear Dr. Justin and Gromacs User, >>> >>> Thank you so much for your helps. >>> >>> When I use charmm36 ff to generate the topology for lipid (DOPC). I got >>> many warning "Warning :Long bond " >>> And after get the topology, the total charge is very high (+888 e for >>> DOPC >>> bilayer have 516 molecular). When I used grompp to generate the .tpr >>> file, >>> I got the many error like this : >>> Error 3379 [file topol_Other_chain_D.itp, line 198252] >>> No defaut U-B types >>> ... >>> Error 2379 [file topol_Other_chain_D.itp, line 98252] >>>No default Proper Dih.type >>> >>> >>> What can I do to modified the topology to get the correct charge and fix >>> the error ? >>> >>> I download dopc.itp from Tieleman's website. I run simulation and all >>> things look fine. People have experiences, please tell me the >>> difference >>> of this topology and the one on the charmm36 force field. >>> >>> >> The files Tieleman provides are united-atom structures that may use a >> different naming convention. They won't have H atoms on the aliphatic >> groups and there is no .hdb entry for DOPC. The ridiculous net charge you >> got for DOPC (which is neutral!) should be an indicator that whatever >> topology you built is utter nonsense. There should also be no warnings >> about missing parameters, so this is further evidence that the topology is >> wrong and the "things look fine" assertion seems totally unfounded to me. >> >> If you want to simulate a simple membrane, use CHARMM-GUI to build it. >> It will be 100% CHARMM compliant and we give you all the necessary input >> files. >> >> >> -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] Charmm 36 parameter file for gromacs
Dear Dr. Justin and Gromacs User, Thank you so much for your helps. When I use charmm36 ff to generate the topology for lipid (DOPC). I got many warning "Warning :Long bond " And after get the topology, the total charge is very high (+888 e for DOPC bilayer have 516 molecular). When I used grompp to generate the .tpr file, I got the many error like this : Error 3379 [file topol_Other_chain_D.itp, line 198252] No defaut U-B types ... Error 2379 [file topol_Other_chain_D.itp, line 98252] No default Proper Dih.type What can I do to modified the topology to get the correct charge and fix the error ? I download dopc.itp from Tieleman's website. I run simulation and all things look fine. People have experiences, please tell me the difference of this topology and the one on the charmm36 force field. Thank you so much Tuong Vy 2015-08-11 23:05 GMT+09:00 Justin Lemkul : > > > On 8/11/15 10:01 AM, Vy Phan wrote: > >> Dear Gromacs users, >> >> On the .itp file on the charmm36 force field, I see the DOPC and other >> lipid which have the [atom][bond] and [ impropers] parameter. I wonder >> where is the parameter for [dihedrals]. >> >> > Angles and dihedrals are automatically generated from the bonded > connectivity. Only mandatory directives are included in the .rtp entries. > > -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] Charmm 36 parameter file for gromacs
Dear Gromacs users, On the .itp file on the charmm36 force field, I see the DOPC and other lipid which have the [atom][bond] and [ impropers] parameter. I wonder where is the parameter for [dihedrals]. please help me! Thank in advance Tuong Vy -- 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] Can not run energy minimization for the protein-lipid system.
Dear Gromacs Users I run membrane protein with DOPC lipip. Without protein, the lipid-ions-water system can run energy minimization. But when I insert protein in the center of that system (I removed the overlapping molecules), but this system can not run. I always got this message. Actually, I do not know where is the error come from. Could someone help me? Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.0e+01 Number of steps= 5000 F-max = inf on atom 89 F-Norm= inf Energy minimization has stopped, but the forces have not converged to the requested precision Fmax < 10 (which may not be possible for your system). It stopped because the algorithm tried to make a new step whose size was too small, or there was no change in the energy since last step. Either way, we regard the minimization as converged to within the available machine precision, given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, but this is often not needed for preparing to run molecular dynamics. WARNING: there may be something wrong with energy file em.edr Found: step=-1, nre=33, nblock=0, time=-1. Trying to skip frame expect a crash though writing lowest energy coordinates. Back Off! I just backed up em.gro to ./#em.gro.1# Polak-Ribiere Conjugate Gradients converged to machine precision in -1 steps, but did not reach the requested Fmax < 10. Potential Energy = 3.8252541e+26 Maximum force =inf on atom 89 Norm of force =inf Thank in advance Phan Vy -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Topology for DOPC lipid Charmm36 ff
Dear Catarina, I *am so sorry. I can run the simulations, n*ow*.* *Thank you* 2015-08-07 17:35 GMT+09:00 Catarina A. Carvalheda dos Santos < c.a.c.dossan...@dundee.ac.uk>: > Hi Phan, > > DOPC is already in the Charmm36 distribution for GROMACS. Check the .rtp > file. > > Cheers, > > On 7 August 2015 at 05:51, Vy Phan wrote: > > > Dear Gromacs users, > > I want to run tranmembrane protein with Gromacs code and using Charmm 36 > > ff. I tried to search the the topology for DOPC, I couldn't find. > > > > Could someone here help me? > > > > Thank in advance > > Phan Vy > > -- > > 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. > > > > The University of Dundee is a registered Scottish Charity, No: SC015096 > > > > > > -- > Catarina A. Carvalheda > > PhD Student > Computational Biology Division > School of Life Sciences > University of Dundee > DD1 5EH, Dundee, Scotland, UK > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Topology for DOPC lipid Charmm36 ff
Dear Gromacs users, I want to run tranmembrane protein with Gromacs code and using Charmm 36 ff. I tried to search the the topology for DOPC, I couldn't find. Could someone here help me? Thank in advance Phan Vy -- 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] .trr file
Hi, Put the command line nstout, nstout (Output control-chapter 5-Gromacs manual) on your mdp file. Phan Vy 2015-06-05 13:36 GMT+09:00 Swapnil Kate : > hello, > > These are my files, in EM step it is generating .trr file and in NVT and > NPT it coulden't. > I am still working on the problem so I could generate trajectory file.can > you please go through and let me the problem.I will keep trying meanwhile > Regards > Swapnil > > > > > On Thursday, 4 June 2015 10:09 PM, Justin Lemkul > wrote: > > > > > On 6/4/15 12:24 PM, Swapnil Kate wrote: > > Hello all, > > Actually I am doing very basic simulations on n-decane.But my problem > is, I can not generate trajectory (.trr) file.Only energy minimization step > is generating that but NVT and NPT simulations coulden't!! > > Is there any settings in .mdp file or there is any other option > avaliable? > > What output-related settings do you have in the EM .mdp file that aren't > in the > subsequent .mdp files? That should tell you what you should be setting to > get > what you want (see also the manual section entitled "Output control." > > -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. > -- 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] Center of mass motion removal
Dear Tsjerk.
I see. Many thanks your explanation.
Tuong Vy
2015-06-03 15:44 GMT+09:00 Tsjerk Wassenaar :
> Hi Tuong Vy,
>
> There is no difference in practice except for raising the error. The
> developers can't try catching all possible foolish things people could try
> with an error. Also, if you think of fooling the program in this way, you
> may be assumed to know what you're doing (and why you wouldn't need to
> worry about flying ice cubes).
>
> Cheers,
>
> Tsjerk
> On Jun 3, 2015 8:23 AM, "Vy Phan" wrote:
>
> > Dear Tsjerk and all,
> > If I set up the comm-mode =None ( COM motion is not removed), i got the
> > Warning : numerical rounding errors can lead to build up of kinetic
> energy
> > of the COM and the simulation can not run.
> > I think comm-mode =None and {comm-mode =Linear , nstcomm > nststeps) is
> > similar meaning.
> > I misunderstand something?
> > Could you explain more?
> >
> > Many Thanks
> > Tuong Vy
> >
> > 2015-06-03 15:11 GMT+09:00 Tsjerk Wassenaar :
> >
> > > Hi Tuong Vy,
> > >
> > > Right. If COMM is removed every N steps and the simulation runs for M
> < N
> > > steps, then COMM will never actually be removed.
> > >
> > > Cheers,
> > >
> > > Tsjerk
> > > On Jun 3, 2015 4:44 AM, "Vy Phan" wrote:
> > >
> > > > Dear all,
> > > > I wonder when I set the comm-mode =Linear , and nstcomm
> > > > (frequency for COM motion removal) > nststeps (maxinum number of
> > steps),
> > > > the MD simulation can be performed.
> > > >
> > > > I think the nstcomm > nsteps mean COM motion is not removed (the MD
> > > > simulation can be not performed)
> > > > Could somebody explain to me ?
> > > >
> > > > Tuong Vy
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
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> > > > posting!
> > > >
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> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > > --
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Re: [gmx-users] Center of mass motion removal
Dear Tsjerk and all,
If I set up the comm-mode =None ( COM motion is not removed), i got the
Warning : numerical rounding errors can lead to build up of kinetic energy
of the COM and the simulation can not run.
I think comm-mode =None and {comm-mode =Linear , nstcomm > nststeps) is
similar meaning.
I misunderstand something?
Could you explain more?
Many Thanks
Tuong Vy
2015-06-03 15:11 GMT+09:00 Tsjerk Wassenaar :
> Hi Tuong Vy,
>
> Right. If COMM is removed every N steps and the simulation runs for M < N
> steps, then COMM will never actually be removed.
>
> Cheers,
>
> Tsjerk
> On Jun 3, 2015 4:44 AM, "Vy Phan" wrote:
>
> > Dear all,
> > I wonder when I set the comm-mode =Linear , and nstcomm
> > (frequency for COM motion removal) > nststeps (maxinum number of steps),
> > the MD simulation can be performed.
> >
> > I think the nstcomm > nsteps mean COM motion is not removed (the MD
> > simulation can be not performed)
> > Could somebody explain to me ?
> >
> > Tuong Vy
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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[gmx-users] epsilon-r
Dear Gromacs Users, I do not know how to set up the epsilon-r and epsilon-rf in simulation with spc model water. I set it as default value (epsilon-r =1 and epsilon-rf =0). Is it right? Thank you so much Tuong Vy -- 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] Center of mass motion removal
Dear all, I wonder when I set the comm-mode =Linear , and nstcomm (frequency for COM motion removal) > nststeps (maxinum number of steps), the MD simulation can be performed. I think the nstcomm > nsteps mean COM motion is not removed (the MD simulation can be not performed) Could somebody explain to me ? Tuong Vy -- 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] Tutorial site down
Dear Justin, I hope all thing will be on its road soon :) Tuong Vy 2015-06-02 23:12 GMT+09:00 Justin Lemkul : > > All, > > Yesterday we experienced a hardware failure on the server that hosts my > GROMACS tutorials. We are aware of the issue and are going to be setting > up a new server. The tutorials may end up on this new server or another; I > haven't decided yet. For the next few days, the tutorials will be > unavailable. > > I apologize for any inconvenience and we will get the materials back up as > soon as possible. > > -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] Making disulfide bonds between protein and glutathion (GSH)
Many thanks Justin :) Tuong Vy 2015-05-28 21:01 GMT+09:00 Justin Lemkul : > > > On 5/27/15 10:23 PM, Vy Phan wrote: > >> Dear Gromas User, >> I want to making disulfide bonds between protein and glutathion (GSH). >> The topology for GSH I got from Produg serve. >> > > Don't do this; the topology will be of very poor quality. See > http://pubs.acs.org/doi/abs/10.1021/ci100335w > > Could you please show me how I can make the disulfide bons between >> protein >> and GSH? >> >> > Add an entry in specbond.dat > > http://www.gromacs.org/Documentation/File_Formats/specbond.dat > > -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] Topology for Ligand from Prodrg server and force field 54a7 for protein
Dear Gromacs Users I use the force field 54a7 for protein. Can I simulate the protein-ligand complex with topology of ligand get from PRODRG server. Thanh in advance Tuong Vy -- 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] Making disulfide bonds between protein and glutathion (GSH)
Dear Gromas User, I want to making disulfide bonds between protein and glutathion (GSH). The topology for GSH I got from Produg serve. Could you please show me how I can make the disulfide bons between protein and GSH? Thank you so much Tuong Vy -- 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] Building topologies manually
Dear Justin, I am so thankful for your reply. I still do not know how I can build the topology for the [image: $\gamma$] -Glu. I want to use gromos force field 54a7. Could you give some more guideline? Tuong Vy 2015-05-28 5:27 GMT+09:00 Justin Lemkul : > > > On 5/27/15 9:41 AM, Vy Phan wrote: > >> Dear Gromacs Users, >> >> I want to simulate the protein s-glutathionylation. The problem is how to >> build the topologies for glutathione ([image: $\gamma$]-Glu-Cys-Gly). >> >> Could someone give me some suggestion and experiences? >> >> > This should be simple to piece together from existing building blocks, but > the particular details depend on the force field you're using. That's a > key component to the process. > > -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] Building topologies manually
Dear Gromacs Users, I want to simulate the protein s-glutathionylation. The problem is how to build the topologies for glutathione ([image: $\gamma$]-Glu-Cys-Gly). Could someone give me some suggestion and experiences? Thank in advance Tuong Vy -- 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] restraint one part of protein
thank you so much Justin Tuong Vy 2015-05-26 20:40 GMT+09:00 Justin Lemkul : > > > On 5/26/15 6:58 AM, Vy Phan wrote: > >> Dear All, >> I got the pdb file from protein Data Bank with some missing loop. I use >> swissmodel to add the missing loop. In energy minimization step, I want to >> relax these loops and restraint the crystal structure. How can I generate >> the restraint file? >> Could someone help for this jobs? >> >> > genrestr with a suitable index group. > > -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] restraint one part of protein
Dear All, I got the pdb file from protein Data Bank with some missing loop. I use swissmodel to add the missing loop. In energy minimization step, I want to relax these loops and restraint the crystal structure. How can I generate the restraint file? Could someone help for this jobs? Tuong Vy -- 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] Run NVT equilibrium
Thank a lot for your clearly explanation. Tuong Vy 2015-05-24 0:28 GMT+09:00 Justin Lemkul : > > > On 5/23/15 10:40 AM, Vy Phan wrote: > >> Dear all, >> I wonder why , on some tutorial, running NVT equilibrium we need only the >> em.gro (the final coordinate of energy minimization step) . why do we not >> need em.edr ? >> >> > Because there's no information in the .edr file that is needed to start > NVT after EM. You only need the minimized coordinates at that point. > > -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] High density
Dear all, My system includes protein and spc water. After running 1000ps NPT equilibrium I got the density is 1010+/-1.25. I hope I can get the density is 1000kg/m3. I run for a long NPT step, I still get around 1010. Is this value is fine ? Do I need to run more? Tuong Vy -- 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] Run NVT equilibrium
Dear all, I wonder why , on some tutorial, running NVT equilibrium we need only the em.gro (the final coordinate of energy minimization step) . why do we not need em.edr ? Thank a lot Tuong VY -- 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] LINSC WARNING
Thank a lot for your suggestion. Tuong VY 2015-05-22 20:21 GMT+09:00 Mark Abraham : > Hi, > > Start by learning what makes a time step stable, e.g. manual 6.8 > > Mark > > On Fri, May 22, 2015 at 10:51 AM Vy Phan wrote: > > > Dear Gromacs Users, > > When I run npt equilibrium, I set the step size is 4fs. I go many LINCS > > WARNING > > "bonds that rotate more than 30 degrees" > > > > > > When I reduce the step size to 2fs. All thing is fine. > > > > Could someone here explain to me? > > Finally, I want to use step size is 4fs. Any suggestions for me? > > > > Thank you > > Tuong Vy > > -- > > 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] LINSC WARNING
Dear Gromacs Users, When I run npt equilibrium, I set the step size is 4fs. I go many LINCS WARNING "bonds that rotate more than 30 degrees" When I reduce the step size to 2fs. All thing is fine. Could someone here explain to me? Finally, I want to use step size is 4fs. Any suggestions for me? Thank you Tuong Vy -- 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] Generate the water box
Dear all, I can generate the cubic box or the rectangular box with gmx solvate -cs water.gro -box but I would like to have the octahedron box.I try many way but I can not. How I can do it? Thank a lot Tuong Vy 2015-05-21 1:49 GMT+09:00 Justin Lemkul : > > > On 5/20/15 11:55 AM, 姚懿 wrote: > >> genbox without adding a protein. >> >> > More specifically (and for 5.0): > > gmx solvate -cs water.gro -box (whatever size is needed) > > -Justin > > On Wed, May 20, 2015 at 9:56 AM, Vy Phan wrote: >> >> Dear Gromacs Users, >>> >>> Can I generate only water on the Gromacs? I need water box only. >>> >>> Thank you >>> Tuong Vy >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >>> posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >>> >> >> >> > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Generate the water box
Dear Gromacs Users, Can I generate only water on the Gromacs? I need water box only. Thank you Tuong Vy -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem control output for checkpoint file
Thank you so much for the suggestion. Tuong Vy 2015-05-19 23:15 GMT+09:00 Mark Abraham : > Hi, > > EM is implemented separately from MD, and since people rarely write enough > trajectory-frame coordinates from EM for I/O to be a serious issue, there's > no good reason to support XTC writing. You can always use trjconv to > post-process out the groups or steps you want, etc. > > Mark > > On Tue, May 19, 2015 at 4:13 PM Justin Lemkul wrote: > > > > > > > On 5/19/15 10:10 AM, Vy Phan wrote: > > > Dear Justin Lemku, > > > I am so thankful for your help > > > Could you please help me more ? > > > Here is the way I control output file for energy minimization step , > > > integrator = cg > > > nstcgsteep = 1000 > > > emtol = 100.0 > > > emstep = 0.01 > > > nsteps = 5000 > > > ; Output control > > > nstxout = 0 > > > nstvout = 0 > > > nstfout = 0 > > > nstenergy = 50 > > > nstlog = 50 > > > nstxout-compressed = 50 > > > > > > But, the parameter file in the mdout.mdp file like this > > > > > > ; OUTPUT CONTROL OPTIONS > > > ; Output frequency for coords (x), velocities (v) and forces (f) > > > nstxout = 50 > > > nstvout = 0 > > > nstfout = 0 > > > ; Output frequency for energies to log file and energy file > > > nstlog = 50 > > > nstcalcenergy= 100 > > > nstenergy= 50 > > > ; Output frequency and precision for .xtc file > > > nstxout-compressed = 0 > > > compressed-x-precision = 1000 > > > > > > > > > I do not know why this happen ? > > > > IIRC you can't write an .xtc during EM, only during actual dynamics. > > There's > > probably some magic that grompp does to translate this, but I've never > > looked > > into it. > > > > -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. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem control output for checkpoint file
Dear Justin Lemku, I am so thankful for your help Could you please help me more ? Here is the way I control output file for energy minimization step , integrator = cg nstcgsteep = 1000 emtol = 100.0 emstep = 0.01 nsteps = 5000 ; Output control nstxout = 0 nstvout = 0 nstfout = 0 nstenergy = 50 nstlog = 50 nstxout-compressed = 50 But, the parameter file in the mdout.mdp file like this ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 50 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file nstlog = 50 nstcalcenergy= 100 nstenergy= 50 ; Output frequency and precision for .xtc file nstxout-compressed = 0 compressed-x-precision = 1000 I do not know why this happen ? Tuong Vy 2015-05-19 22:39 GMT+09:00 Justin Lemkul : > > > On 5/19/15 9:24 AM, Vy Phan wrote: > >> Dear Gromacs Users! >> I am a beginner. I am looking for the command line corresponding with >> nstcheckpoint (control the output of the checkpoint file) in the Gomacs >> 5.0.4 but I coudn't find. And when I check the log file, I also can not >> recognize what command line which controls cpt file. >> >> > Read the mdrun help information: > > -cpt (15) Checkpoint interval (minutes) > > The second question, when I run energy minimization I got only one frame, >> I >> try to reduce the frequency saving the coordinates but I still get the >> same >> result (it look the control output did not working ). I want to save more >> frame to see what happen in the energy minimization step . Can some one >> help me? >> >> > If EM finishes in one step, either (1) the structure was already minimized > or (2) EM failed. The .log file will tell you happened. > > The third question, I want to generate only the xtc file (I do not want to >> generate the trr file). What command I need to use for Gromacs 5.0.4 ? (I >> know the command constxtcout when I search on google, but I can not find >> the information for it on gromacs manual 5.0.4) >> >> > nstxout-compressed is the current keyword. Suppress the .trr by setting > nstxout, nstvout, and nstfout to zero. > > Make sure you do some basic tutorial material; these elements are all > covered by most, if not all, of 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.
Re: [gmx-users] The octahedron problem
Dear Tsjerk Wassenaar Can I display it on the VMD ? Thank a lot Tuong Vy 2015-05-19 20:22 GMT+09:00 Tsjerk Wassenaar : > Hi Tuong Vy, > > An octahedral or dodecahedral box is pretty tricky. I have a Pymol script > for generating them, but it will probably require some more work... > > Cheers, > > Tsjerk > On May 19, 2015 13:18, "Vy Phan" wrote: > > > Dear Gromacs Users, > > I have the problem with generating the octahedron box. I always get the > > rectangular box (using VMD) > > When I searched on the gmx maillist, I saw some people met same problem. > > Is problem is normal in gromacs? > > > > After run simulation, I can display the trajectory on VMD by using the > > command trjconv -pbc mol -ur compact for converting the system. But I can > > not display the octahedron box after solvated system. > > > > Could someone help me ? > > > > Tuong Vy > > -- > > 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] Problem control output for checkpoint file
Dear Gromacs Users! I am a beginner. I am looking for the command line corresponding with nstcheckpoint (control the output of the checkpoint file) in the Gomacs 5.0.4 but I coudn't find. And when I check the log file, I also can not recognize what command line which controls cpt file. The second question, when I run energy minimization I got only one frame, I try to reduce the frequency saving the coordinates but I still get the same result (it look the control output did not working ). I want to save more frame to see what happen in the energy minimization step . Can some one help me? The third question, I want to generate only the xtc file (I do not want to generate the trr file). What command I need to use for Gromacs 5.0.4 ? (I know the command constxtcout when I search on google, but I can not find the information for it on gromacs manual 5.0.4) Thank you so much and best regards, Tuong Vy -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] The octahedron problem
Dear Gromacs Users, I have the problem with generating the octahedron box. I always get the rectangular box (using VMD) When I searched on the gmx maillist, I saw some people met same problem. Is problem is normal in gromacs? After run simulation, I can display the trajectory on VMD by using the command trjconv -pbc mol -ur compact for converting the system. But I can not display the octahedron box after solvated system. Could someone help me ? Tuong Vy -- 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.
