[gmx-users] Using -all flag in g_angle command
Hello everyone, I simulated an NADH molecule. I want to check how each of the dihedral angles changes during the simulation. In other words, I want to plot a graph of individual (not average) dihedral angles versus time. To do so, I created an index file using the following command: $ mk_angndx -s full.tpr -n angle.ndx -type dihedral Next, I used the g_angle command as follows: $ g_angle -f full.xtc -n angle.ndx -type dihedral -all However, this command generated only one output file angdist.xvg. The -ov flag generates angles in degrees; but, it gives values in average and I want the same plot for individual angles. Please suggest how to proceed. Thank you. -- 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] Applying restraints into 'secondary structure' of a Protein
Dear Mark,
Thanks for your reply.
Does it do that in just-water also? If the structure is not rock-stable in
water, then your required minimum amount of sampling goes up immensely,
because you will have to sample many such transitions to observe adsorption
(when/if it happens).
Yes it does.
The main issue is that this proteins are intrinsically disordered proteins on
water, so on water this protein moves randomly.
That’s why at first i placed the protein near to the hydrophilic interface of
the POPC membrane in order to ‘force it’ to interact with it, sadly without
luck. This is the reason why i’m in the need to find a way to force the protein
to maintain its tertiary structure.
Looking into literature i found different papers, where the authors propose an
umbrella sampling strategy in order to map the reaction coordinate of the
overall process.
http://pubs.rsc.org/EN/content/articlelanding/2013/sm/c3sm51990b/unauth#!divAbstract
http://www.sciencedirect.com/science/article/pii/S0005273612002581
what do you think about this strategy?
Since i don’t have access to a big computer center, i don’t know if i’ll be
able to run this kind of simulations (I’m currently performing around ~40ns on
system with about 90k - 120k atoms, and this system; POPC+water
molecules+protein, is around 110k).
Thanks for your help
--
Carlos Navarro Retamal
Bioinformatics Engineering
Ph. D (c) Applied Sciences.
Center of Bioinformatics and Molecular Simulations. CBSM
University of Talca
Av. Lircay S/N, Talca, Chile
T: (+56) 712201 798
E: carlos.navarr...@gmail.com or cnava...@utalca.cl
On January 13, 2015 at 3:34:10 AM, Mark Abraham
(mark.j.abra...@gmail.commailto:mark.j.abra...@gmail.com) wrote:
On Tue, Jan 13, 2015 at 3:45 AM, Carlos Navarro Retamal cnava...@utalca.cl
wrote:
Dear gromacs users,
In order to analyse the adsorption process of a Protein (amphipatic
protein) into a POPC membrane i’m placing several conformations at
different distances of respective membrane (on different simulations) and
performed regular MD simulations.
My problem is that during the production phase the protein start to move
randomly, loosing its amphipatic nature (and in that way, moving far from
the POPC hydrophobic interface).
Does it do that in just-water also? If the structure is not rock-stable in
water, then your required minimum amount of sampling goes up immensely,
because you will have to sample many such transitions to observe adsorption
(when/if it happens).
So, my question is: Is there a way to maintain the tertiary structure
('overall’) of the protein (in my particular case, two alpha helices joined
by a loop) allowing it to maintain its amphipatic nature during the
simulation, helping it to interact peripherally to the hydrophobic
interface of the membrane?
The traditional hacks for doing this include distance and orientation
restraints between parts of your protein. Whether those mask relevant
motion is difficult to say, since you're not going to be able to afford the
calculation that shows what you'd observe if the restraints were absent (or
you'd just do it that way).
In any case, maybe this is not the ideal strategy to analyse the
interaction between this two macromolecules (protein interacting
peripherally with respect to a bilayer membrane), so if you think in
something else please feel free to make any suggestions.
The brute-force sampling required for such a study seems to require an
amount of current resources that is impossibly large. But I don't know of
an alternative.
Mark
Best regards,
Carlos
--
Carlos Navarro Retamal
Bioinformatics Engineering
Ph. D (c) Applied Sciences.
Center of Bioinformatics and Molecular Simulations. CBSM
University of Talca
Av. Lircay S/N, Talca, Chile
T: (+56) 71 2 201tel://T:%20(+56)%2071%202%20201 798
E: cmailto:francisco.ada...@gmail.comarlos.navarr...@gmail.com or
cnava...@utalca.clmailto:fadas...@utalca.cl
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Re: [gmx-users] clustering using gromos method
Thanks for the reply Xavier. Cheers, Adriana *** Dra. Adriana D. Garro Química Medicinal Facultad de Química, Bioquímica y Farmacia Universidad Nacional de San Luis IMASL-CONICET San Luis, Argentina Tel..:+54 266 4424689 int 6153 e-mail...: adga...@unsl.edu.ar e-mail...: adrianagarr...@gmail.com ** 2015-01-12 17:12 GMT+01:00 XAvier Periole x.peri...@rug.nl: with the gromos method the criteria is the RMSD between the structure of the objects given to cluster …. two neighbours are two structures that are within this cutoff (eg. 0.25) obviously defining an RMSD between the two objects should make sense. On Jan 12, 2015, at 4:56 PM, Adriana Garro adrianagarr...@gmail.com wrote: Dear All, I am working on a Coarse Grained model (Martini force field), I have a trajectory file and I am trying to do a clustering procedure using the gromos method, this is the command line I used g_cluster -f dynamic.xtc -s dynamic.tpr -o cluster.xpm -clid cluster-id-over-time.xvg -cl clusters.pdb -cutoff 0.25 -method gromos -skip 10 and it finished well, I got more than 40 clusters, of course if I vary the cutoff this number changes but I am not sure what is the more optimal value for my system. In fact I dont understand very well what is the meaning of this parameter. I have read this gromos: use algorithm as described in Daura et al. (Angew. Chem. Int. Ed. *1999*, 38, pp 236-240). Count number of neighbors using cut-off, take structure with largest number of *neighbors* with all its neighbors as cluster and eliminate it from the pool of clusters. Repeat for remaining structures in pool. But still...what neighbors means in this context? If someone can clarify this for me, I'd really appreciate it. (I cant acces to the original publication). Thanks in advance. Adriana -- 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] clustering using gromos method
Yes, should work. Check that the central structures make sense. At some point this option was not giving the correct structure. On Jan 13, 2015, at 1:32 PM, Adriana Garro adrianagarr...@gmail.com wrote: Another question just to be sure that I get what I want. I want the structure with the smallest average distance to the others (The center of a cluster) for each cluster written in the clusters.pdb file (option -cl), but after calculation I get this message in the log file Writing middle structure for each cluster to clusters.pdb is it ok?? the command line I used g_cluster -f dynamic.xtc -s dynamic.tpr -o cluster.xpm -minstruct 20 -sz cluster-sizes.xvg -clid cluster-id-over-time.xvg -cl clusters.pdb -cutoff 0.3 -method gromos -skip 10 -dist rms-distribution.xvg -noav Thanks for your time! Adriana *** Dra. Adriana D. Garro Química Medicinal Facultad de Química, Bioquímica y Farmacia Universidad Nacional de San Luis IMASL-CONICET San Luis, Argentina Tel..:+54 266 4424689 int 6153 e-mail...: adga...@unsl.edu.ar e-mail...: adrianagarr...@gmail.com ** 2015-01-13 9:46 GMT+01:00 Adriana Garro adrianagarr...@gmail.com: Thanks for the reply Xavier. Cheers, Adriana *** Dra. Adriana D. Garro Química Medicinal Facultad de Química, Bioquímica y Farmacia Universidad Nacional de San Luis IMASL-CONICET San Luis, Argentina Tel..:+54 266 4424689 int 6153 e-mail...: adga...@unsl.edu.ar e-mail...: adrianagarr...@gmail.com ** 2015-01-12 17:12 GMT+01:00 XAvier Periole x.peri...@rug.nl: with the gromos method the criteria is the RMSD between the structure of the objects given to cluster …. two neighbours are two structures that are within this cutoff (eg. 0.25) obviously defining an RMSD between the two objects should make sense. On Jan 12, 2015, at 4:56 PM, Adriana Garro adrianagarr...@gmail.com wrote: Dear All, I am working on a Coarse Grained model (Martini force field), I have a trajectory file and I am trying to do a clustering procedure using the gromos method, this is the command line I used g_cluster -f dynamic.xtc -s dynamic.tpr -o cluster.xpm -clid cluster-id-over-time.xvg -cl clusters.pdb -cutoff 0.25 -method gromos -skip 10 and it finished well, I got more than 40 clusters, of course if I vary the cutoff this number changes but I am not sure what is the more optimal value for my system. In fact I dont understand very well what is the meaning of this parameter. I have read this gromos: use algorithm as described in Daura et al. (Angew. Chem. Int. Ed. *1999*, 38, pp 236-240). Count number of neighbors using cut-off, take structure with largest number of *neighbors* with all its neighbors as cluster and eliminate it from the pool of clusters. Repeat for remaining structures in pool. But still...what neighbors means in this context? If someone can clarify this for me, I'd really appreciate it. (I cant acces to the original publication). Thanks in advance. Adriana -- 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. -- 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] Transition matrix generation
On Jan 13, 2015, at 1:27 AM, pratibha kapoor wrote: Hi, I have done MD simulations on my system and have generated clusters of my interest. Now, I would like to look at the transitions between different clusters and henceforth the most probable pathway. Is there any inbuild software that can do this? I have read some of the papers which have analyzed using markov state model followed by transition path sampling. Any idea how all these can be done using some inbuild scripts? Thanks I'm not aware of any Markov State Modeling tools built directly into Gromacs, but there are several excellent third party tools. I've used MSMBuilder before and it will read gromacs trajectory files natively via MDTraj: http://msmbuilder.org There's also EMMA, which looks like it just takes the projection of your trajectory onto the state space: http://pythonhosted.org/pyEMMA/ Hope that helps, Josh -- 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] Virial Calculation in Gromacs Source Code
Dear All, As part of my work I am looking at making modifications to calculation of the virial in gromacs. I have spent some time making myself a bit familiar with the gromacs source and I've looked at the doxygen generated docs and through the various pages on the developer section of the website but I'm still at a bit of a loss as to where to start making these modifications. I've found a calc_vir.c source file and tried to follow the backwards and I also see references to the virial in do_md and global_stat but I'm struggling to put it all together. Are there any more sources of information about the source code that I haven't found or can anyone point me to where I need to be looking to make changes to the virial calculation? Thanks in advance, Adam Hardy PhD Student School of Engineering and Physical Sciences Heriot-Watt University Edinburgh EH14 4AS, UK - We invite research leaders and ambitious early career researchers to join us in leading and driving research in key inter-disciplinary themes. Please see www.hw.ac.uk/researchleaders for further information and how to apply. Heriot-Watt University is a Scottish charity registered under charity number SC000278. -- 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] clustering using gromos method
Another question just to be sure that I get what I want. I want the structure with the smallest average distance to the others (The center of a cluster) for each cluster written in the clusters.pdb file (option -cl), but after calculation I get this message in the log file Writing middle structure for each cluster to clusters.pdb is it ok?? the command line I used g_cluster -f dynamic.xtc -s dynamic.tpr -o cluster.xpm -minstruct 20 -sz cluster-sizes.xvg -clid cluster-id-over-time.xvg -cl clusters.pdb -cutoff 0.3 -method gromos -skip 10 -dist rms-distribution.xvg -noav Thanks for your time! Adriana *** Dra. Adriana D. Garro Química Medicinal Facultad de Química, Bioquímica y Farmacia Universidad Nacional de San Luis IMASL-CONICET San Luis, Argentina Tel..:+54 266 4424689 int 6153 e-mail...: adga...@unsl.edu.ar e-mail...: adrianagarr...@gmail.com ** 2015-01-13 9:46 GMT+01:00 Adriana Garro adrianagarr...@gmail.com: Thanks for the reply Xavier. Cheers, Adriana *** Dra. Adriana D. Garro Química Medicinal Facultad de Química, Bioquímica y Farmacia Universidad Nacional de San Luis IMASL-CONICET San Luis, Argentina Tel..:+54 266 4424689 int 6153 e-mail...: adga...@unsl.edu.ar e-mail...: adrianagarr...@gmail.com ** 2015-01-12 17:12 GMT+01:00 XAvier Periole x.peri...@rug.nl: with the gromos method the criteria is the RMSD between the structure of the objects given to cluster …. two neighbours are two structures that are within this cutoff (eg. 0.25) obviously defining an RMSD between the two objects should make sense. On Jan 12, 2015, at 4:56 PM, Adriana Garro adrianagarr...@gmail.com wrote: Dear All, I am working on a Coarse Grained model (Martini force field), I have a trajectory file and I am trying to do a clustering procedure using the gromos method, this is the command line I used g_cluster -f dynamic.xtc -s dynamic.tpr -o cluster.xpm -clid cluster-id-over-time.xvg -cl clusters.pdb -cutoff 0.25 -method gromos -skip 10 and it finished well, I got more than 40 clusters, of course if I vary the cutoff this number changes but I am not sure what is the more optimal value for my system. In fact I dont understand very well what is the meaning of this parameter. I have read this gromos: use algorithm as described in Daura et al. (Angew. Chem. Int. Ed. *1999*, 38, pp 236-240). Count number of neighbors using cut-off, take structure with largest number of *neighbors* with all its neighbors as cluster and eliminate it from the pool of clusters. Repeat for remaining structures in pool. But still...what neighbors means in this context? If someone can clarify this for me, I'd really appreciate it. (I cant acces to the original publication). Thanks in advance. Adriana -- 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] analysing charmm trajectories
Dear all, I'd like to use the gromacs analysis tool to analyse a simulation performed with charmm. I installed the latest gromacs version (5.0.4), in which both .dcd trajectories and all the files read also by vmd should be readable. After that, the trajectory is correctly processed by gromacs, but I've troubles with the analysis tools that need .tpr files. As suggested in some previous posts, I've generated a fake file .top with vmd, useful to produce a new .tpr suitable for the analysis. I also installed the charmm36 forcefield in the gmx top directory (the same that I used in the simulation). When I use grompp to generate a .tpr, I get this error: Fatal error: Unknown cmap torsion between atoms 5 7 9 22 24 Among the possible solutions I found the use of this patch, but this was concerning an older vs of gromacs: “0001-Fix-pdb2gmx-merge-cmap.patch”, so I skipped it during installation. I do not understand if this error it's a matter of forcefield or it depends on something else. Does anyone could help me to figure-out the origin of the error and how to fix the problem? Also pdb2gmx is not working because some atoms are not found in the forcefield (such as CAY, used by charmm for methylated methionine). Manipulating the forcefield would fix both the problems? In this case how should I proceed? I'd really appreciate any suggestion! Thank you very much in advance! Chiara -- 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] trjconv mismatch in number of atoms
Dear Experts, I am running a trjconv from xtc files to pdb file but have got this error: Fatal error: Index[4622] 135978 is larger than the number of atoms in the trajectory file (36976). There is a mismatch in the contents of your -f, -s and/or -n files. I don't know where the origin of the Problem, the index.ndx was created from md.gro file, the *.xtc (8 Proteins in a box, so I type #1 to have the index of 8 Proteins, each Protein has 4622 Atoms). The trajectory has 36976 Atoms which is 4622 * 8 and 135978 is the total number of Atoms in the System. I would really appreciate for your help. SIncerely, Jennifer -- 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] Pressure coupling error
Hi all, I’m receiving this error from grompp: ERROR 1 [file npt.mdp, line 50]: Pressure coupling not enough values (I need 2) I think I’ve inserted in the .mdo the required values: integrator = md tinit= 0 dt = 0.002 nsteps = 5000;100ns comm-mode= Linear nstcomm = 10 comm-grps= System nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstenergy= 80 nstxtcout= 750 xtc-precision= 1500 xtc-grps = System energygrps = WAT MET HEX nstlist = 20 ns_type = grid pbc = xyz periodic_molecules = no rlist= 1.1 coulombtype = PME rcoulomb = 1.1 ;cutoff-scheme = Verlet vdw-type = Cut-off rvdw = 1.5 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 6 ewald_rtol = 1e-5 optimize_fft = yes Tcoupl = Nose-hoover tc-grps = WAT MET HEX tau_t= 0.1 0.1 0.1 ref_t= 298 298 298 Pcoupl = Parrinello-Rahman Pcoupltype = semiisotropic tau_p= 1.0 1.0 ref_p = 1.0 1.0 compressibility = 4.5e-5 gen_vel = no gen_temp = 298 gen_seed = 173529 constraints = all-bonds constraint-algorithm = Lincs lincs-order = 4 lincs-iter = 1 -- 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] Pressure coupling error
You also need to add a second value for compressibility as you have done for tau-p and ref-p. Adam Hardy PhD Student School of Engineering and Physical Sciences Heriot-Watt University Edinburgh EH14 4AS, UK From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Riccardo Concu [ric.co...@gmail.com] Sent: 13 January 2015 15:28 To: gmx-us...@gromacs.org Subject: [gmx-users] Pressure coupling error Hi all, I’m receiving this error from grompp: ERROR 1 [file npt.mdp, line 50]: Pressure coupling not enough values (I need 2) I think I’ve inserted in the .mdo the required values: integrator = md tinit= 0 dt = 0.002 nsteps = 5000;100ns comm-mode= Linear nstcomm = 10 comm-grps= System nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstenergy= 80 nstxtcout= 750 xtc-precision= 1500 xtc-grps = System energygrps = WAT MET HEX nstlist = 20 ns_type = grid pbc = xyz periodic_molecules = no rlist= 1.1 coulombtype = PME rcoulomb = 1.1 ;cutoff-scheme = Verlet vdw-type = Cut-off rvdw = 1.5 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 6 ewald_rtol = 1e-5 optimize_fft = yes Tcoupl = Nose-hoover tc-grps = WAT MET HEX tau_t= 0.1 0.1 0.1 ref_t= 298 298 298 Pcoupl = Parrinello-Rahman Pcoupltype = semiisotropic tau_p= 1.0 1.0 ref_p = 1.0 1.0 compressibility = 4.5e-5 gen_vel = no gen_temp = 298 gen_seed = 173529 constraints = all-bonds constraint-algorithm = Lincs lincs-order = 4 lincs-iter = 1 -- 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. - We invite research leaders and ambitious early career researchers to join us in leading and driving research in key inter-disciplinary themes. Please see www.hw.ac.uk/researchleaders for further information and how to apply. Heriot-Watt University is a Scottish charity registered under charity number SC000278. -- 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] Virial Calculation in Gromacs Source Code
Hi, No doubt you've seen Appendix B of the manual. (Yes, we need to work more on docs organization.) Relevant data structures and functions mostly include the letters fshift for shift forces. The use of git grep is very much your friend here. Mark On Tue, Jan 13, 2015 at 3:22 PM, Hardy, Adam ah...@hw.ac.uk wrote: Dear All, As part of my work I am looking at making modifications to calculation of the virial in gromacs. I have spent some time making myself a bit familiar with the gromacs source and I've looked at the doxygen generated docs and through the various pages on the developer section of the website but I'm still at a bit of a loss as to where to start making these modifications. I've found a calc_vir.c source file and tried to follow the backwards and I also see references to the virial in do_md and global_stat but I'm struggling to put it all together. Are there any more sources of information about the source code that I haven't found or can anyone point me to where I need to be looking to make changes to the virial calculation? Thanks in advance, Adam Hardy PhD Student School of Engineering and Physical Sciences Heriot-Watt University Edinburgh EH14 4AS, UK - We invite research leaders and ambitious early career researchers to join us in leading and driving research in key inter-disciplinary themes. Please see www.hw.ac.uk/researchleaders for further information and how to apply. Heriot-Watt University is a Scottish charity registered under charity number SC000278. -- 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] Pressure coupling error
Now it works. Thank you -Original Message- From: Hardy, Adam Sent: Tuesday, January 13, 2015 4:57 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Pressure coupling error You also need to add a second value for compressibility as you have done for tau-p and ref-p. Adam Hardy PhD Student School of Engineering and Physical Sciences Heriot-Watt University Edinburgh EH14 4AS, UK From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Riccardo Concu [ric.co...@gmail.com] Sent: 13 January 2015 15:28 To: gmx-us...@gromacs.org Subject: [gmx-users] Pressure coupling error Hi all, I’m receiving this error from grompp: ERROR 1 [file npt.mdp, line 50]: Pressure coupling not enough values (I need 2) I think I’ve inserted in the .mdo the required values: integrator = md tinit= 0 dt = 0.002 nsteps = 5000;100ns comm-mode= Linear nstcomm = 10 comm-grps= System nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 1000 nstenergy= 80 nstxtcout= 750 xtc-precision= 1500 xtc-grps = System energygrps = WAT MET HEX nstlist = 20 ns_type = grid pbc = xyz periodic_molecules = no rlist= 1.1 coulombtype = PME rcoulomb = 1.1 ;cutoff-scheme = Verlet vdw-type = Cut-off rvdw = 1.5 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 6 ewald_rtol = 1e-5 optimize_fft = yes Tcoupl = Nose-hoover tc-grps = WAT MET HEX tau_t= 0.1 0.1 0.1 ref_t= 298 298 298 Pcoupl = Parrinello-Rahman Pcoupltype = semiisotropic tau_p= 1.0 1.0 ref_p = 1.0 1.0 compressibility = 4.5e-5 gen_vel = no gen_temp = 298 gen_seed = 173529 constraints = all-bonds constraint-algorithm = Lincs lincs-order = 4 lincs-iter = 1 -- 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. - We invite research leaders and ambitious early career researchers to join us in leading and driving research in key inter-disciplinary themes. Please see www.hw.ac.uk/researchleaders for further information and how to apply. Heriot-Watt University is a Scottish charity registered under charity number SC000278. -- 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] Gromacs precision and the precision of values set in the mdp file
Hello Gromacs users, What is the precision limit for values entered in an mdp file for a single precision gromacs simulation? Does this increase when using gromacs is compiled in double precision? Best, Eric -- 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] trjconv mismatch in number of atoms
On 1/13/15 10:15 AM, Jennifer Vo wrote: Dear Experts, I am running a trjconv from xtc files to pdb file but have got this error: Fatal error: Index[4622] 135978 is larger than the number of atoms in the trajectory file (36976). There is a mismatch in the contents of your -f, -s and/or -n files. I don't know where the origin of the Problem, the index.ndx was created from md.gro file, the *.xtc (8 Proteins in a box, so I type #1 to have the index of 8 Proteins, each Protein has 4622 Atoms). The trajectory has 36976 Atoms which is 4622 * 8 and 135978 is the total number of Atoms in the This means you chose Protein as the only group saved in the .xtc (xtc-grps/compressed-x-grps). If you want to do analysis, you need to re-create your index file and perhaps make a matching .tpr file. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] analysing charmm trajectories
On 1/13/15 8:18 AM, Chiara Parravicini wrote: Dear all, I'd like to use the gromacs analysis tool to analyse a simulation performed with charmm. I installed the latest gromacs version (5.0.4), in which both .dcd trajectories and all the files read also by vmd should be readable. After that, the trajectory is correctly processed by gromacs, but I've troubles with the analysis tools that need .tpr files. As suggested in some previous posts, I've generated a fake file .top with vmd, useful to produce a new .tpr suitable for the analysis. I also installed the charmm36 forcefield in the gmx top directory (the same that I used in the simulation). When I use grompp to generate a .tpr, I get this error: Fatal error: Unknown cmap torsion between atoms 5 7 9 22 24 Among the possible solutions I found the use of this patch, but this was concerning an older vs of gromacs: “0001-Fix-pdb2gmx-merge-cmap.patch”, so I skipped it during installation. I do not understand if this error it's a matter of forcefield or it depends on something else. Does anyone could help me to figure-out the origin of the error and how to fix the problem? Also pdb2gmx is not working because some atoms are not found in the forcefield (such as CAY, used by charmm for methylated methionine). Manipulating the forcefield would fix both the problems? In this case how should I proceed? I'd really appreciate any suggestion! So the .top that VMD wrote is probably wrong in some way, but if you're just using it to do analysis and not actually run a simulation, I'd say you can probably remove the offending CMAP term from the .top and proceed. -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.
