[gmx-users] Problem restarting job 2016.4 with gromacs 2019-4
Dear Gromacs users We just installed Gromacs 2019.4 And I get an error restarting free energy jobs (pull) run with Gromacs 2016.4 I' m using one GPU gmx mdrun -nt 20 -s umbrella3_60ns.tpr -cpi umbrella3.cpt -deffnm umbrella3 -pf pullf-umbrella3.xvg -px pullx-umbrella3.xvg GROMACS version:2019.4 Precision: single Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) GPU support:CUDA SIMD instructions: AVX2_256 Using 1 MPI thread Using 20 OpenMP threads 1 GPU selected for this run. Fatal error: Mismatch between number of energies in run input (52) and checkpoint file (51 or 51). And of course the run restarts OK with Gromacs 2016.4 ?? Anybody got an idea or bug fix ? Regards Serge Crouzy -- 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] Restart dynamics when trr files removed
Hello Jon and Justin I had a MD simulation "dyn" running for 46 ns (actually it's 30 umbrella simulations using pull code) I did try the -cpi option and my calculation seems to have restarted correctly renaming the files dyn.part0003 But just running gmx mdrun -cpi -noappend does not allow me to tell the number of additional steps I want in my dynamics - So right now it's running 46 more ns (the original mdp and tpr file) which is not reasonable because I have 100s of calculations to run - I want to be able to specify 5 ns more for instance Usually I use gmx convert-tpr - extend 5000 which builds a new tpr with which I can restart with -cpi And running without a checkpoint file, Justin is not what I want - I really need to restart my dynamics after 46 ns, just I don't want the trr files - (I've got all the other files all right) - There should be a trick to restart without writing to a trr file... Isn't there ? Thanks again for your help Serge Crouzy PhD HDR Groupe de Modélisation et Chimie Théorique Laboratoire de Chimie et Biologie des Métaux Département des Interfaces pour l'Energie, la Santé et l'Environnement Institut de Recherche Interdisciplinaire de Grenoble CEA Grenoble UMR CEA/CNRS/UJF 5249 17, rue des martyrs 38054 Grenoble Cedex 9 Bat. K pièce 110 Tel (33) 438782963 Fax (33) 438785487 http://big.cea.fr/drf/big/english/CBM/GMCT -Message d'origine- De : gromacs.org_gmx-users-boun...@maillist.sys.kth.se De la part de gromacs.org_gmx-users-requ...@maillist.sys.kth.se Envoyé : lundi 13 mai 2019 15:23 À : gromacs.org_gmx-users@maillist.sys.kth.se Objet : gromacs.org_gmx-users Digest, Vol 181, Issue 30 Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than "Re: Contents of gromacs.org_gmx-users digest..." Today's Topics: 1. Gromacs error while running energy minimization step (Muneeswaran S) 2. Re: ligand in water (Bratin Kumar Das) 3. Re: water mediated Hbond (Bratin Kumar Das) 4. nmr distance restraints (Eiso AB) 5. Restart dynamics when trr files removed (CROUZY Serge 119222) 6. Re: Restart dynamics when trr files removed (John Whittaker) -- Message: 1 Date: Mon, 13 May 2019 17:36:36 +0530 From: Muneeswaran S To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Gromacs error while running energy minimization step Message-ID: Content-Type: text/plain; charset="UTF-8" I got the following error while running the gromacs *NOTE: disabling dynamic load balancing as it is only supported with dynamics, not with integrator 'steep'.Using 16 MPI threadsUsing 4 OpenMP threads per tMPI threadOn host localhost.localdomain 2 GPUs auto-selected for this run.Mapping of GPU IDs to the 16 GPU tasks in the 16 ranks on this node: PP:0,PP:0,PP:0,PP:0,PP:0,PP:0,PP:0,PP:0,PP:1,PP:1,PP:1,PP:1,PP:1,PP:1,PP:1,PP:1---Program: gmx mdrun, version 2018.6Source file: src/gromacs/utility/filestream.cpp (line 115)Function:gmx::internal::FileStreamImpl::FileStreamImpl(const char*, const char*)MPI rank:12 (out of 16)System I/O error:Failed to compile NBNXN kernels for GPU #Quadro P620 Could not open file '/usr/share/gromacs/opencl/nbnxn_ocl_kernels.cl <http://nbnxn_ocl_kernels.cl>'Reason: No such file or directory (call to fopen() returned error code 2)For more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors <http://www.gromacs.org/Documentation/Errors>* -- Message: 2 Date: Mon, 13 May 2019 18:15:27 +0530 From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in> To: gmx-us...@gromacs.org Subject: Re: [gmx-users] ligand in water Message-ID: Content-Type: text/plain; charset="UTF-8" Hi The procedure you are following is not ok. Generate the co-ordinate file of ligand and the topology parameter file. Setup the box and add water to it. Lastly do energy minimisation. On Thu 9 May, 2019, 2:33 PM RAHUL SURESH, wrote: > Hi Users. > > I want to simulate ligand in the water box. I prepared a water > molecule and started with pdb2gmx and then planned to follow protein-ligand > tutorial. > Unfortunately ended up with an error in gro file format. Have check > every possibility but still couldn't
[gmx-users] Restart dynamics when trr files removed
Dear Gromacs users I ran long MD simulations ( 50ns) with nstxout=5000 resulting in very large .trr files Realizing that I did not need these files (xtc enough), I removed them hoping to regenerate necessary restart files from a new gmx grompp and corrected mdp file (with nstxout=0)... But NO - I can't restart the simulation from 50 ns on without trr files - Whatever tricks I seem to have tried to fool the controls I hope someone can tell me how I can solve my problem - Even if it is recompiling the source to remove the flag checking that the trr file is absent Thanks for your help ! Serge Crouzy PhD HDR Groupe de Modélisation et Chimie Théorique Laboratoire de Chimie et Biologie des Métaux Département des Interfaces pour l'Energie, la Santé et l'Environnement Institut de Recherche Interdisciplinaire de Grenoble CEA Grenoble UMR CEA/CNRS/UJF 5249 17, rue des martyrs 38054 Grenoble Cedex 9 Bat. K pièce 110 Tel (33) 438782963 Fax (33) 438785487 http://big.cea.fr/drf/big/english/CBM/GMCT -- 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] 4. Re: 5. Re: 3. Re: Strange pullx coordinates (PMF
Hello Justin I still don't understand where Gromacs takes the x coordinates in the output pmf with g_wham If I run g_wham with tpr-files and pullf-files without the pullx-files -it tpr-files.dat -if pullf-files.dat I get a profile which means that g_wham does not take the X-coordinates in the pullx (I don't give them), but in the tpr files ... So what X-coordinates are stored in the tpr-files ? Then if I use -it tpr-files.dat -ix pullx-files.dat Where does g_wham take the forces and which x coordinates does it take : those from the tpr or those from the pullx ? Moreover when I restart my simulations, I regenerate new tpr files For instance to add 10 more ns gmx convert-tpr -s umbrella10ns.tpr -extend 1 -o umbrella20ns.tpr gmx mdrun -s umbrella20ns.tpr -cpi xxx.cpt If I run g_wham after this simulation, which tpr should I use ? Can you please explain the role of these tpr in g_wham calculations? Thanks a lot On 11/5/18 5:07 AM, CROUZY Serge 119222 wrote: > Hello Justin- > In MY pullx first column is Time and second column is absolute > coordinate of the COM of the pulled group Maybe we are missing an option > which would print X and dX in the pullx files - one of the pull-print stuffs > ???!!.. In that case too bad we would have tons of "bad" pull files Printing > the reaction coordinate (dX) should be the default .. Don't you think so ? > Hence my problem with wham using absolute coordinate instead of actual > distance between the two centers of mass What do you suggest to retrieve the > actual values of my reaction coordinate without rerrunning everything ? It should be straightforward to apply a systematic shift to the values in the output PMF curve. But I don't know how you've set up your pull code to get such output in the first place. The absolute position of group0 should be totally irrelevant. -Justin > Serge > > * -- 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] 5. Re: 3. Re: Strange pullx coordinates (PMF calculations)
Hello Justin- In MY pullx first column is Time and second column is absolute coordinate of the COM of the pulled group Maybe we are missing an option which would print X and dX in the pullx files - one of the pull-print stuffs ???!!.. In that case too bad we would have tons of "bad" pull files Printing the reaction coordinate (dX) should be the default .. Don't you think so ? Hence my problem with wham using absolute coordinate instead of actual distance between the two centers of mass What do you suggest to retrieve the actual values of my reaction coordinate without rerrunning everything ? Serge Dear Justin Thanks for your fast answer OK for the larger group0 COM but as you say my reaction coordinate is the distance between the two COMs - The problem being that in the profile.xvg file the X coordinate reflects the box sizes and thus I can't superimpose the profiles coming from Simulations 1) and 2) - I need to have in the pmf profile X coordinates equal to the distance between COMs not absolute distance as it is now .. How can I correct the x coordinate in the pmfs so that they represent my real reaction coordinate which is the distance between COMs? Isn't it a strange choice to write the absolute coordinates of the COM in the pullx files instead of the real reaction coordinate we all need ? Now do I have to reread all my trajs, calculate the center of mass of the X coordinate of the COM of DNA (my fixed molecule) and subtract it at each line of the pullx files ... This does not make sense ... Thanks a lot On 10/31/18 11:43 AM, CROUZY Serge 119222 wrote: > Dear gromacs users > > I've been running gromacs for several years, and enjoyed it.. > I've been running PMF calculations for protein DNA interactions without > problems until recently: > Now I'm puzzled with the X coordinates being written in the pullx > files (and thus taken as reaction coordinate values in the PMF). This > is my problem > > I run two simulations 1) protein A moving away from DNA > DNA---A-> along x > 2) same protein A moving away > from DNA in the presence of protein B: B-DNA---A -> along x In 2) A > and B interact slightly and I expect to see a slight difference in the > profiles for pulling A away In both simulations I'm pulling on center > of mass of A away from center of mass of DNA (force along X only) > > My problem is that the x pulling coordinates in simulation 2) (in the pullx > files) are around 9 A larger than in simulation 1). Consequence: the profiles > are shifted along x by around 9 A. This is not logical to me since my > reaction coordinate is distance between com of A and com of DNA which should > be the same !! > It's as if the size of the simulation box (around 10 A larger in 2) to > accommodate B ) mattered .. ?! (I'm running PME with PBC in water...) Yes, that makes sense. The first column(s) in pullx.xvg are whatever (x,y,z) components of the group0 COM. If your box is larger, then naturally the position is different. What should not be different is the relative DNA-A distance, which is the actual reaction coordinate. Absolute coordinates of any one species don't really matter. -Justin -- Message: 5 Date: Wed, 31 Oct 2018 13:24:45 -0400 From: Justin Lemkul To: gmx-us...@gromacs.org Subject: Re: [gmx-users] 3. Re: Strange pullx coordinates (PMF calculations) (Justin Lemkul) Message-ID: <10376386-bbb5-fa99-9743-8786e0069...@vt.edu> Content-Type: text/plain; charset=utf-8; format=flowed On 10/31/18 12:54 PM, CROUZY Serge 119222 wrote: > Dear Justin > > Thanks for your fast answer > OK for the larger group0 COM but as you say my reaction coordinate is > the distance between the two COMs - The problem being that in the profile.xvg > file the X coordinate reflects the box sizes and thus I can't superimpose the > profiles coming from Simulations 1) and 2) - I need to have in the pmf > profile X coordinates equal to the distance between COMs not absolute > distance as it is now .. How can I correct the x coordinate in the pmfs so > that they represent my real reaction coordinate which is the distance between > COMs? > Isn't it a strange choice to write the absolute coordinates of the COM in the > pullx files instead of the real reaction coordinate we all need ? Now do I > have to reread all my trajs, calculate the center of mass of the X coordinate > of the COM of DNA (my fixed molecule) and subtract it at each line of the > pullx files ... This does not make sense ... There are two columns in pullx.xvg - X and dX, the reference position and the distance along the biasing potential. WHAM should be using the latter; the absolute position in space should not matter. You can also
[gmx-users] 3. Re: Strange pullx coordinates (PMF calculations) (Justin Lemkul)
Dear Justin Thanks for your fast answer OK for the larger group0 COM but as you say my reaction coordinate is the distance between the two COMs - The problem being that in the profile.xvg file the X coordinate reflects the box sizes and thus I can't superimpose the profiles coming from Simulations 1) and 2) - I need to have in the pmf profile X coordinates equal to the distance between COMs not absolute distance as it is now .. How can I correct the x coordinate in the pmfs so that they represent my real reaction coordinate which is the distance between COMs? Isn't it a strange choice to write the absolute coordinates of the COM in the pullx files instead of the real reaction coordinate we all need ? Now do I have to reread all my trajs, calculate the center of mass of the X coordinate of the COM of DNA (my fixed molecule) and subtract it at each line of the pullx files ... This does not make sense ... Thanks a lot On 10/31/18 11:43 AM, CROUZY Serge 119222 wrote: > Dear gromacs users > > I've been running gromacs for several years, and enjoyed it.. > I've been running PMF calculations for protein DNA interactions without > problems until recently: > Now I'm puzzled with the X coordinates being written in the pullx > files (and thus taken as reaction coordinate values in the PMF). This > is my problem > > I run two simulations 1) protein A moving away from DNA > DNA---A-> along x > 2) same protein A moving away > from DNA in the presence of protein B: B-DNA---A -> along x In 2) A > and B interact slightly and I expect to see a slight difference in the > profiles for pulling A away In both simulations I'm pulling on center > of mass of A away from center of mass of DNA (force along X only) > > My problem is that the x pulling coordinates in simulation 2) (in the pullx > files) are around 9 A larger than in simulation 1). Consequence: the profiles > are shifted along x by around 9 A. This is not logical to me since my > reaction coordinate is distance between com of A and com of DNA which should > be the same !! > It's as if the size of the simulation box (around 10 A larger in 2) to > accommodate B ) mattered .. ?! (I'm running PME with PBC in water...) Yes, that makes sense. The first column(s) in pullx.xvg are whatever (x,y,z) components of the group0 COM. If your box is larger, then naturally the position is different. What should not be different is the relative DNA-A distance, which is the actual reaction coordinate. Absolute coordinates of any one species don't really matter. -Justin -- 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] Strange pullx coordinates (PMF calculations)
Dear gromacs users I've been running gromacs for several years, and enjoyed it.. I've been running PMF calculations for protein DNA interactions without problems until recently: Now I'm puzzled with the X coordinates being written in the pullx files (and thus taken as reaction coordinate values in the PMF). This is my problem I run two simulations 1) protein A moving away from DNA DNA---A-> along x 2) same protein A moving away from DNA in the presence of protein B: B-DNA---A -> along x In 2) A and B interact slightly and I expect to see a slight difference in the profiles for pulling A away In both simulations I'm pulling on center of mass of A away from center of mass of DNA (force along X only) My problem is that the x pulling coordinates in simulation 2) (in the pullx files) are around 9 A larger than in simulation 1). Consequence: the profiles are shifted along x by around 9 A. This is not logical to me since my reaction coordinate is distance between com of A and com of DNA which should be the same !! It's as if the size of the simulation box (around 10 A larger in 2) to accommodate B ) mattered .. ?! (I'm running PME with PBC in water...) I hope this is clear enough and somebody can tell me what's happening ?! Thanks a lot for your valuable answers Serge Serge Crouzy PhD HDR Groupe de Modélisation et Chimie Théorique Laboratoire de Chimie et Biologie des Métaux Institut de Biosciences et Biotechnologies de Grenoble CEA Grenoble UMR CEA/CNRS/UJF 5249 17, rue des martyrs 38054 Grenoble Cedex 9 Bat. K pièce 110 Tel (33) 438782963 Fax (33) 438785487 http://big.cea.fr/drf/big/english/CBM/GMCT -- 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] Distance between centers of mass
Hi Justin Bouncing back on your early answer about gmx distance, I noticed something strange (to me) I'musing the same instruction for a protein file prot.gro gmx distance ... -select "com of group 'Protein' plus com of group 'Ligand'" and now I'm running umbrella sampling with pull code starting from prot.gro pulling groups are the same 'Protein' and 'Ligand' and strange the first line in the pullx.xvg file does not give the same distance as gmx distance !! Any idea why ? Thx -Message d'origine- De : gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] De la part de Justin Lemkul Envoyé : jeudi 2 mars 2017 23:12 À : gmx-us...@gromacs.org Objet : Re: [gmx-users] Distance between centers of mass On 3/2/17 4:15 PM, ÁLVARO RODRIGO RUIZ FERNÁNDEZ wrote: > Dear GROMACS users: > > How can I calculate the distance between centers of mass of two > residues in time with gmx distance?, I do not understand the sentence > "com of resname AAA plus com of resname BBB" from the manual, pag 241 . > Thanks. > > This is simply the selection syntax for doing exactly what you describe. You can select by residue name, number, etc. or by an existing index group, e.g. gmx distance ... -select "com of group 'Protein' plus com of group 'Ligand'" -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] Significance of abscissa in pmf from 2 reactions coordinates
Dear Gromacs users I'm running pull simulations using two reaction coordinates 1) distance between c.o.m. of G1 and G2 (G1 and G2 groups of atoms) 2) distance between c.o.m. of G3 and G2 same pulling force (umbrella potential), 25 windows At the end of the treatment by g_wham I can have 3 profiles 1 corresponding to first distance (-is option) : G(x1) 2 corresponding to second distance : G(x2) 3 full profile with the two distances : G(xtot??) The significance of the abscissa in profiles 1 and 2 is clear, but what about in the combined profile (xtot)? Since I'm pulling along X only (Fy=Fz=0) I would suggest to correct the xtot given in profile 3 by 0.5(x1+x2).. Is this correct ? Thanx for your input Serge -- 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] Post-analysis of residue residue interactions
Yes that's a good idea I didn't know about different energy groups I'll try that Thanks a lot Mark -Message d'origine- De : gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] De la part de Mark Abraham Envoyé : vendredi 3 février 2017 14:19 À : gmx-us...@gromacs.org Objet : Re: [gmx-users] Post-analysis of residue residue interactions Hi, You can have more than one energy-group pair-of-interest per rerun. That will compute more pairwise combinations that are not of interest, requiring more sophisticated use of gmx energy, but this will run a lot faster than the I/O you're saving. e.g. energygrps = A ResInter1 ResInter2 ... ResInterN for some chunk size of N distinct residues of B. IIRC there's a cap of 64 energy groups because of how they were used in the implementation of the old group scheme. Mark On Thu, Feb 2, 2017 at 2:41 PM CROUZY Serge 119222 <serge.cro...@cea.fr> wrote: > > Dear gromacs users > > We've run umbrella sampling simulations (with pull) of > proteinA/ProteinB dimer turning into two separate monomers We have 25 > simulation windows each of 10 ns MD (1000 frames) and proteins > containing 132 residues We now want to calculate interaction energy > (VDW Elec) between each residu of B (1 by 1) and all residues of A (as > a whole) to understand which residues most contribute to the PMF > > The way we do that is described below : > for (( f=0; f<=25; f++ ))(all frames) > for (( res =1; res<=132; res++ )) (all residues) > make_ndx ResInter define residue number > in B : Resinter > gmx_mpi grompp build tpr define new > energy groups energygrps = A ResInter > mpirun -np 8 gmx_mpi mdrun -rerun umbrella$f.xtc rerun > dynamics on the 1000 frames > g_energyaverage energy > between Resinter and total A protein > done > done > > that's 25*132*1000 = 33 10⁵ energy calculations and particularly time > consuming 132*25 = 3300 times rereading the trajectories > > I was wondering is there a more efficient way to do this ? For > instance reading each trajectory only once instead of 132 times That's > basically exchanging loop order > for (( f=0; f<=25; f++ )) (all frames) >mpirun -np 8 gmx_mpi mdrun -rerun umbrella$f.xtc >for (( res =1; res<=132; res++ )) > g_energy >done > done > but this does not seem possible because the interacting groups have to > be defined before calling md rerun > > Any idea would be greatly appreciated > > Thanx > > Serge Crouzy > > -- > 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] Post-analysis of residue residue interactions
Dear gromacs users We've run umbrella sampling simulations (with pull) of proteinA/ProteinB dimer turning into two separate monomers We have 25 simulation windows each of 10 ns MD (1000 frames) and proteins containing 132 residues We now want to calculate interaction energy (VDW Elec) between each residu of B (1 by 1) and all residues of A (as a whole) to understand which residues most contribute to the PMF The way we do that is described below : for (( f=0; f<=25; f++ ))(all frames) for (( res =1; res<=132; res++ )) (all residues) make_ndx ResInter define residue number in B : Resinter gmx_mpi grompp build tpr define new energy groups energygrps = A ResInter mpirun -np 8 gmx_mpi mdrun -rerun umbrella$f.xtc rerun dynamics on the 1000 frames g_energyaverage energy between Resinter and total A protein done done that's 25*132*1000 = 33 10⁵ energy calculations and particularly time consuming 132*25 = 3300 times rereading the trajectories I was wondering is there a more efficient way to do this ? For instance reading each trajectory only once instead of 132 times That's basically exchanging loop order for (( f=0; f<=25; f++ )) (all frames) mpirun -np 8 gmx_mpi mdrun -rerun umbrella$f.xtc for (( res =1; res<=132; res++ )) g_energy done done but this does not seem possible because the interacting groups have to be defined before calling md rerun Any idea would be greatly appreciated Thanx Serge Crouzy -- 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] Adding FE2+ parameters
Hello Hannes I'm perfectly aware how you need to be careful in using metal parameters - checking for which solvent and which coordination they have been created for. In my case structural metal coordinated to protein amino acids... I did try to see in Li/Merz parameters which line could resemble the parameters in Gromacs for Zn2+ but with no success - This brings me back to the original question, where do Zn parameters in Gromacs 54a7 come from ? Knowing this I could try deduce parameters for Fe2+ Thanx Serge Crouzy PhD HDR Groupe de Modélisation et Chimie Théorique Laboratoire de Chimie et Biologie des Métaux Institut de Biosciences et Biotechnologies de Grenoble CEA Grenoble UMR CEA/CNRS/UJF 5249 17, rue des martyrs 38054 Grenoble Cedex 9 Bat. K pièce 110 Tel (33)0438782963 Fax (33)0438785487 http://big.cea.fr/drf/big/CBM/GMCT -Message d'origine- De : gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] De la part de Hannes Loeffler Envoyé : mardi 10 janvier 2017 17:38 À : gromacs.org_gmx-users@maillist.sys.kth.se Cc : gmx-us...@gromacs.org Objet : Re: [gmx-users] Adding FE2+ or FE3+ into the system What are you planning to do with those parameters? You could have a look into the Li/Merz parameters (and papers!) available with the AmberTools (may not have been converted yet to Gromacs formats and the 12-6-4 sets would need support in the code). Generally, you should be wary when using simple ion force fields and check carefully how they have been parameterised and what for. Distinguishing different valencies of the same transition metal atom with only vdW/Coulomb parameters will most likely not capture their complex chemistry. On Tue, 10 Jan 2017 16:24:47 + CROUZY Serge 119222 <serge.cro...@cea.fr> wrote: > I'm interested as well in knowing how to get decent parameters for > Fe2+ > > From gromacs-5.1.2/share/top/gromos54a7.ff/ffnonbonded.itp > We have Zn2+ (What is a reference for these parameters ?) > > name bondtype mass charge ptype CA > ;name at.num mass charge ptype c6 c12 > ZN2+ 30 0.000 0.000 A 0.0004182025 9.4400656e-09 > > From which I deduced > if LJ = v(rij)=C(12)/r12 - C(6)/r6 = A/r^12 -C/r^6 to be compared to > the standard V=4*eps*[(sig/r)^12 - (sig/r)^6] A =4*eps*sig^12 > C=4*eps*sig^6 > sig = (A/C)^1/6 > eps=C^2 / (4 A) > For Zn sig=0.168112 eps=4.631677 kJ/mol > > But no Fe2+ > > Regards > > Serge Crouzy PhD HDR > Groupe de Modélisation et Chimie Théorique Laboratoire de Chimie et > Biologie des Métaux Institut de Biosciences et Biotechnologies de > Grenoble CEA Grenoble UMR CEA/CNRS/UJF 5249 17, rue des martyrs > 38054 Grenoble Cedex 9 > Bat. K pièce 110 > Tel (33)0438782963 > Fax (33)0438785487 > http://big.cea.fr/drf/big/CBM/GMCT > > > > -Message d'origine- > De : gromacs.org_gmx-users-boun...@maillist.sys.kth.se > [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] De la part > de liming_52 Envoyé : mardi 10 janvier 2017 16:54 À : > gmx-us...@gromacs.org Objet : [gmx-users] Adding FE2+ or FE3+ into > the system > > Dear gromacs users, > > I want to compare the protein in the buffers with FE2+ and FE3+, > respectively. > > How can I add FE2+ or FE3+ into the system? What is the command? > > Thanks in advance. > > > > > > -- > > With my best wishes, > Ming Li, PhD > Chinese Academy of Agricultural Sciences, Beijing, China -- 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] Adding FE2+ or FE3+ into the system
I'm interested as well in knowing how to get decent parameters for Fe2+ >From gromacs-5.1.2/share/top/gromos54a7.ff/ffnonbonded.itp We have Zn2+ (What is a reference for these parameters ?) name bondtype mass charge ptype CA ;name at.num mass charge ptype c6 c12 ZN2+ 30 0.000 0.000 A 0.0004182025 9.4400656e-09 >From which I deduced if LJ = v(rij)=C(12)/r12 - C(6)/r6 = A/r^12 -C/r^6 to be compared to the standard V=4*eps*[(sig/r)^12 - (sig/r)^6] A =4*eps*sig^12 C=4*eps*sig^6 sig = (A/C)^1/6 eps=C^2 / (4 A) For Zn sig=0.168112 eps=4.631677 kJ/mol But no Fe2+ Regards Serge Crouzy PhD HDR Groupe de Modélisation et Chimie Théorique Laboratoire de Chimie et Biologie des Métaux Institut de Biosciences et Biotechnologies de Grenoble CEA Grenoble UMR CEA/CNRS/UJF 5249 17, rue des martyrs 38054 Grenoble Cedex 9 Bat. K pièce 110 Tel (33)0438782963 Fax (33)0438785487 http://big.cea.fr/drf/big/CBM/GMCT -Message d'origine- De : gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] De la part de liming_52 Envoyé : mardi 10 janvier 2017 16:54 À : gmx-us...@gromacs.org Objet : [gmx-users] Adding FE2+ or FE3+ into the system Dear gromacs users, I want to compare the protein in the buffers with FE2+ and FE3+, respectively. How can I add FE2+ or FE3+ into the system? What is the command? Thanks in advance. -- With my best wishes, Ming Li, PhD Chinese Academy of Agricultural Sciences, Beijing, China -- 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] where do Zinc parameters come from ?
Hello users Can anyone tell me where the LJ parameters for Zn2+ come from in the Gromacs gromos54a7.ff force field ? (Literature reference for instance) ;name at.num mass charge ptype c6 c12 ZN2+ 30 0.000 0.000 A 0.0004182025 9.4400656e-09 I'm actually looking for parameters for Fe2+ which I could try to derive using the same approach (I know these nonbonded parameters will remain a poor approximation of the mertal behavior but I'm only interested in keeping the metal site "geometrically sound") Thanks -- 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] Free energy profiles with Pull code : dimer/dimer interactions
Dear gromacs users In previous mail on the list Justin argued about free energy calculations with Pull code that: "For general protein-ligand complexes, it is *NOT* appropriate to assume one-dimensional pulling or applying position restraints to the protein. Our paper (from which the tutorial was derived) describes the somewhat unique case we were dealing with. " In my case, I'm calculating the profile for dimer dissociation in a tetramer of proteins pulling on 1 dimer in direction X (because the tetramer is oriented in a such a way that X is the principal axis) while the other dimer is harmonically restrained (BB atoms only) I don't see how this could be done differently; although I'm hoping that the free energy will result from the sole force between dimer/dimer atoms: the restraint on one dimer should not affect the result .. As long as they do not prevent the fluctuations (breathing) necessary for an almost reversible extraction of one dimer from the tetramer. Is there a paper describing the possible effect of these restraints on the profile ? (I suppose if one dimer is completely fixed, the energy barrier for extraction will increase dramatically because its residues won't be allowed to adjust while the partner dimer is pulled out) Thanks for your input Serge Crouzy PhD HDR Groupe de Modélisation et Chimie Théorique Laboratoire de Chimie et Biologie des Métaux Institut de Biosciences et Biotechnologies de Grenoble CEA Grenoble UMR CEA/CNRS/UJF 5249 17, rue des martyrs 38054 Grenoble Cedex 9 Bat. K pièce 110 Tel (33)0438782963 Fax (33)0438785487 http://big.cea.fr/drf/big/CBM/GMCT -- 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't find alchemical-gromacs.py
Dear gromacs users I'm following the alchemistry.org gromacs4.6 example on ethanol solvation free energy I've run the simulations and I'm now at the stage of the analysis I installed pymbar.git and pymbar-examples.git But in the alchemical-free-energy directory I find alchemical_analysis.py but no alchemical-gromacs.py !! When I try to run alchemical_analysis.py on my ethanol data with -f ./ethanol. it doesn't work (returns -f: invalid integer value) meaning that alchemical_analysis.py and alchemical-gromacs.py are probably different - Where do I find alchemical-gromacs.py ?? Thx a lot Serge Crouzy PhD HDR Groupe de Modélisation et Chimie Théorique Laboratoire de Chimie et Biologie des Métaux Institut de Biosciences et Biotechnologies de Grenoble CEA Grenoble UMR CEA/CNRS/UJF 5249 17, rue des martyrs 38054 Grenoble Cedex 9 Bat. K pièce 110 Tel (33)0438782963 Fax (33)0438785487 http://big.cea.fr/drf/big/CBM/GMCT 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] Pull group coordinates not expected in pullx files
Dear Gromacs users I'm running umbrella sampling simulations using 2 reaction coordinates: 1 between protein chain A and protein chains BC and the other between chain D and same chains BC (harmonically restrained with DPOSRES) Restraints along X only with 500 kj/mol force Things run OK but when I use gmx_mpi wham -it tpr-files.dat -if pullf-files.dat -o -hist -bins 500 -unit kCal -v I get messages in the ouput like: File umbrella0.tpr, 2 coordinates, geometry "distance", dimensions [Y N N], (1 dimensions) Pull group coordinates not expected in pullx files. crd 0) k = 500 position = 2.19717 crd 1) k = 500 position = 2.02589 Reading pull force file with pull geometry distance and 1 pull dimensions Expecting these columns in pull file: 0 reference columns for each individual pull coordinate 1 data columns for each pull coordinate With 2 pull groups, expect 3 columns (including the time column) Found 12501 times and 2 force sets pullf-umbrella0.xvg File umbrella1.tpr, 2 coordinates, geometry "distance", dimensions [Y N N], (1 dimensions) ... Is this normal : what does this "Pull group coordinates not expected in pullx files", mean ?? Thanks ; Pull code pull = yes pull_ngroups = 3 pull_ncoords = 2 pull_group1_name = Chain_BC pull_group2_name = Chain_A pull_coord1_groups = 1 2 pull_coord1_type = umbrella ; harmonic biasing force pull_coord1_geometry = distance ; simple distance increase pull_coord1_dim = Y N N pull_coord1_rate = 0.0 pull_coord1_k = 500 ; kJ mol^-1 nm^-2 pull_coord1_start = yes ; define initial COM distance > 0 pull_group3_name = Chain_D ; moving pull_coord2_groups = 1 3 pull_coord2_type = umbrella ; harmonic biasing force pull_coord2_geometry = distance ; simple distance increase pull_coord2_dim = Y N N ; pull in X pull_coord2_rate = 0.0 pull_coord2_k = 500 ; kJ mol^-1 nm^-2 pull_coord2_start = yes ; define initial COM distance > 0 -- 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 somebody explain how to set (XY) hexagonal symmetry pbc in gromacs ?
Hello Gromacs users Going from Charmm to Gromacs, I'm trying to simulate a membrane protein inserted into a membrane : I already got the gro and topol file for gromacs for my entire system : Prot + lipids + Water - minimization in rectangular pbc also works fine Now I'm stuck on how to tell Gromacs to respect hexagonal symmetry (nice way to lower number of water molecules and lipids in my system) ? membrane is in the XY plane, Z is principal axis of the inserted protein crystal define in CHARMM as CRYSTAL DEFINE HEXA 78 78 127 90.0 90.0 120.0 So my unit cell is a hexagone in the XY plane (39 Angstrom side) Reading previous exchanges on the forum I guess the first stage could be something like gmx editconf -f system -o out -bt tric -box 7.8 7.8 12.7 -angles 90 90 120 (I don't know why triclinic would do the trick) But what next ? Any help greatly appreciated -- 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] Mutation on membrane protein - Charmm36 for Gromacs
Hello Gromacs users I'd like to use Gromacs to find free energy change in a membrane protein upon single-residue mutation Does anyone have proper forcefield files for doing this ? LIke Charmm36_AA_MUTATION_FORCEFIELD for mutated proteins mixed with charmm36.ff_4.5.7 for lipids ? (I've already got a membrane protein inserted in a membrane built and energy minimized with CHARMM) This would be of GREAT help -- 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] Reference file for harmonic restraints
Hi all, I'm running several sequential minimizations and MD simulations with gromacs after translation of part of my system (the rest being harmonically restrained) and I'm looking for a way to specify unique reference coordinates for all simulations The way I understand Gromacs, you define a posres.itp file called by a #define in the .mdp but the system coordinates used for the restraints are always those read at the start of the run. This is not what I want.. I need to read coordinates to be used as reference (like the REF array in CHARMM) and run all my subsequent simulations setting harmonic restraints to these reference coordinates... Is there an easy way to do this ? Thanks all for your help Serge Crouzy PhD HDR Groupe de Modélisation et Chimie Théorique Laboratoire de Chimie et Biologie des Métaux Institut de Biosciences et Biotechnologies de Grenoble CEA Grenoble UMR CEA/CNRS/UJF 5249 17, rue des martyrs 38054 Grenoble Cedex 9 Bat. K pièce 110 Tel (33)0438782963 Fax (33)0438785487 http://big.cea.fr/drf/big/CBM/GMCT -- 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.
