Re: [gmx-users] Separate structure from box
On Tue, Mar 20, 2018 at 2:30 AM, rose rahmani <rose.rhm...@gmail.com> wrote: > Hi, > I want to extract a structure in a box, i mean i want to extract a sheet > from the box of solution, because i dont have any separated .gro file from > my sheet. How can i do that? > Try creating an index file using "gmx make_ndx" to create an index group containing just the atoms you want. Then use "gmx trjconv" to output a file only containing that group. See the "-h" flag for both of those commands. -- James "Wes" Barnett Postdoctoral Research Scientist Department of Chemical Engineering Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> Columbia University w.barn...@columbia.edu http://wbarnett.us -- 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] Free Energy solvation generate multiple dhdl.xvg output files
It sounds like you are only running one free energy simulation. You need to
run one simulation for each lambda (changing "init-lambda-state" in your
mdp file) and name the dhdl xvg file a different name for each one.
On Mon, Mar 19, 2018 at 8:30 AM, Javier Luque Di Salvo <
jluquedisa...@gmail.com> wrote:
> Dear Gromacs users,
> I am trying to run Free Energy calculations of a single ion in water (to
> calculate its solvation energy). Since this is a new topic for me, I am
> following the tutorial 'Solvation free energy of ethanol' (easily find in
> google). The three steps work well without erros (1-energy minimization,
> 2-equilibration, 3-lambda (de)coupling) but I am not obtaining the separate
> dhdl.xvg files after the step 3, only a single output file run.xvg. The
> reason for this is that in the tutorial, a script named mklambdas.sh is
> used to generate such separate files in separate folders. Since I would
> like to keep track of the .mdp strings and understand how they work, I am
> not using this script, instead I am trying to properly define mdp commands:
>
> _
> ; Free energy variables
> free-energy = yes
> couple-moltype = NH4
> couple-lambda0 = none
> couple-lambda1 = vdwq
> couple-intramol = no
> init-lambda = -1
> init-lambda-state= 0
> delta-lambda = 0
> nstdhdl = 50
> fep-lambdas = 0.0 0.2 0.4 0.6 0.8 0.9 1.0
> mass-lambdas =
> coul-lambdas =
> vdw-lambdas =
> bonded-lambdas =
> restraint-lambdas=
> temperature-lambdas =
> calc-lambda-neighbors= 1
> init-lambda-weights =
> dhdl-print-energy= no
> sc-alpha = 1.0
> sc-power = 1
> sc-r-power = 6
> sc-sigma = 0.3
> sc-coul = no
> separate-dhdl-file = yes
> dhdl-derivatives = yes
> dh_hist_size = 0
> dh_hist_spacing = 0.1
> _
>
> When trying to use "gmx bar -f run.xvg -g run.edr -o bar.xvg" I get this
> error:
> ___
> run.xvg: Ignoring set 'pV (kJ/mol)'.
> run.xvg: 0.0 - 200.0; lambda = 0
> dH/dl & foreign lambdas:
> dH/dl (fep-lambda) (2001 pts)
> delta H to 0 (2001 pts)
> delta H to 0.2 (2001 pts)
>
> Opened run.edr as single precision energy file
> Reading energy frame 0 time0.000
> ---
> Program: gmx bar, version 2016.4
> Source file: src/gromacs/gmxana/gmx_bar.cpp (line 3286)
> Fatal error:
> Did not find delta H information in file run.edr
>
>
> This is the run.xvg output file:
>
>
> # Command line:
> # gmx mdrun -ntmpi 2 -ntomp 8 -pin on -v -deffnm run
> # gmx mdrun is part of G R O M A C S:
> #
> # S C A M O R G
> #
> @title "dH/d\xl\f{} and \xD\f{}H"
> @xaxis label "Time (ps)"
> @yaxis label "dH/d\xl\f{} and \xD\f{}H (kJ/mol [\xl\f{}]\S-1\N)"
> @TYPE xy
> @ subtitle "T = 300 (K) \xl\f{} state 0: fep-lambda = 0."
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "dH/d\xl\f{} fep-lambda = 0."
> @ s1 legend "\xD\f{}H \xl\f{} to 0."
> @ s2 legend "\xD\f{}H \xl\f{} to 0.2000"
> @ s3 legend "pV (kJ/mol)"
> 0. -530.14746 0.000 -106.84067 9.7838984
> 0.1000 -177.17302 0.000 -33.945797 9.7844772
> 0.2000 -158.46501 0.000 -30.541293 9.7854595
> 0.3000 -143.72632 0.000 -27.669909 9.7857714
> (...)
>
>
>
>
> Could you guide me through a proper string definition in the mdp options to
> get separate files, in order to use the BAR algorithm afterwards?
>
> Best regards
>
> *Javier*
> --
> 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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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
--
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
Columbia University
w.barn...@columbia.edu
http://wbarnett.us
--
Gromacs Users mailing list
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Re: [gmx-users] Fwd: MMPBSA
On Fri, Feb 9, 2018 at 8:14 AM, RAHUL SURESH <drrahulsur...@gmail.com> wrote: > Dear all > > I have carried out a protein ligand simulation for 50ns and performed a > PBSA calculation for 10-20ns trajectory. I get a positive binding energy. > How can I tackle it..? > > Thank you > > I think you haven't received in responses because it's unclear what you're asking or what your problem is. You ran some kind of simulation and did a PBSA calculation (not familiar with that) and got a positive binding energy. You'll have to add more details on what you are attempting to achieve, how you are trying to do so (perhaps including input scripts), and what the exact problem is. Wes -- James "Wes" Barnett Postdoctoral Research Scientist Department of Chemical Engineering Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> Columbia University w.barn...@columbia.edu http://wbarnett.us -- 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] PCA mathematical information
On Tue, Feb 6, 2018 at 5:11 AM, edesantis <edesan...@roma2.infn.it> wrote: > Dear gromacs users, > > I am a PhD student in biophysics, > I am trying to preform principal component analysis on my simulations with > the aim to understand if there are present correlated motions during the > dynamics. > > I an not expert of this kind of analysis, > I was studying different tutorials and I saw that it is common to filter > the trajectory to show only the motion along some eigenvectors (gmx anaig > -filt -first -last) > > I didn't understand what is the mathematical operation behind this > operation > > any of you can help me? > Emiliano, There is a paragraph in the GROMACS reference manual which cites a paper which uses this method. I suggest starting with that paper and looking at the background there and the references it cites as well. -- James "Wes" Barnett Postdoctoral Research Scientist Department of Chemical Engineering Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> Columbia University w.barn...@columbia.edu http://wbarnett.us -- 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] hydration free energy
On Fri, Jan 5, 2018 at 2:29 PM, <asaffa...@post.tau.ac.il> wrote: > Thanks for discussion. I am waiting already few days for anyfing reply. > The technique of calculation in the file job.sh. The value of coul-λ is > uniformely increasing from 0 to 1 with the step 0.02 for 50 first λ-steps > and in the same way for vdw-λ last 50 λ-steps. The problem is in the last > trajectory with λ=1 there are no coulomb and vdw intermolecular > interactions with the estimate of the entropy according BAR method > S=62204236256674537472.00 kT. The neigbouring state used in BAR with λ=0.99 > contains no coulomb and some remaining vdw force. Therefore I consider that > overlapping of atoms can't produce this error. It happens only then > opposite coulomb charges overcome vdw in nearly decoupled state. Therefore > there is no need in soft-core interactions because all coulomb is decupling > previously to vdw. > I made the search in archive and this problem was discussed sometimes, but > didn't found clear answer for my case. Now I decided to run the cycle in > the reversed order from decoupled state to real interactions. > > > --- > > You're welcome. > > If there are no vdW and Coul it still calculates the average energy, which > without soft-core technique can be very large when atoms overlap. > You can read > http://www.sciencedirect.com/science/article/pii/S0010465516303411 > > Eq. (2) and the following text etc. > > You can try a soft-core technique to see if it is better. > > Best, > Asaf > Quoting dgfd dgdfg <roin...@mail.ru>: > > Hi, >> >>> >>> Do you know which values of lambdas are used? >>> Are you using a soft-core technique? >>> >>> Asaf >>> >> Thanks for discussion. I am waiting already few days for anyfing reply. >> The technique of calculation in the file job.sh. The value of coul- λ is >> uniformely increasing from 0 to 1 with the step 0.02 for 50 first λ- steps >> and in the same way for vdw- λ last 50 λ- steps. The problem is in the >> last trajectory with λ=1 there are no coulomb and vdw intermolecular >> interactions with the estimate of the entropy according BAR method >> S=62204236256674537472.00 kT. The neigbouring state used in BAR with >> λ=0.99 contains no coulomb and some remaining vdw force. Therefore I >> consider that overlapping of atoms can't produce this error. It happens >> only then opposite coulomb charges overcome vdw in nearly decoupled state. >> Therefore there is no need in soft-core interactions because all coulomb is >> decupling previously to vdw. >> I made the search in archive and this problem was discussed sometimes, >> but didn't found clear answer for my case. Now I decided to run the cycle >> in the reversed order from decoupled state to real interactions. >> >> Have you tried other FE estimate algorithms (i.e. thermodynamic integration, MBAR, etc.). Look into the project "alchemical-analysis". It's a python script that will give you some good visualizations on what is happening at that last step (it's compatible with GROMACS output files). There's an associated paper with it as well. Also double check that you are somehow not mistakingly leaving on some kind of interaction that is blowing up after everything else is decoupled. James "Wes" Barnett Postdoctoral Research Scientist Department of Chemical Engineering Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> Columbia University w.barn...@columbia.edu http://wbarnett.us -- 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 through one direction
On Tue, Nov 28, 2017 at 12:25 PM, ali akgün <ali.akgunp...@gmail.com> wrote: > Hi, > > Can i generate mdp file for pressure through one direction system.For > example: > > Ref pressure: > > X direction:1.0 bar > Other direction: 0.0 bar > Yes, see the options here: http://manual.gromacs.org/documentation/2016.4/user-guide/mdp-options.html -- James "Wes" Barnett Postdoctoral Research Scientist Department of Chemical Engineering Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> Columbia University w.barn...@columbia.edu http://wbarnett.us -- 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] how to output intramolecular pair interaction parameters
On Thu, Nov 16, 2017 at 3:07 PM, Srinivasa Ramisetti < s.b.ramise...@leeds.ac.uk> wrote: > This is continuation to my previous question. I used gmx dump to output > the 1-4 intramolecular interaction parameters. I could get the c6 and c12 > values for all the list of 1-4 pair nteractions within my top file. > However, I could not understand the following lines in the output > information under the ffparams starting from functype[0] to functype[63]. I > do not understand how these 64 of c6,c12 values are related to 36 atoms (8 > atom types) that belong to my System. Could anyone explain me how can I > know which functype belongs to a particular atom/atom type? > You have 8 atomtypes, which means 8 sigmas and 8 epsilons . Here it is just iterating through those atomtypes, combining the sigmas and epsilons according to the combination rule in your force field, and then calculating and storing c6 and c12 in memory (8x8=64). I'm not sure what order it processes things in though. Try doing some of the combining by hand and see what matches up. -- James "Wes" Barnett Postdoctoral Research Scientist Department of Chemical Engineering Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> Columbia University w.barn...@columbia.edu http://wbarnett.us -- 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] how to output intramolecular pair interaction parameters
On Thu, Nov 16, 2017 at 1:42 PM, Srinivasa Ramisetti < s.b.ramise...@leeds.ac.uk> wrote: > Hi Micholas, > > > Thanks for your reply. I tried as you suggested and could not find the > information on pair interaction parameters. > > > I will try to rephrase my question so that it is clear to everyone. I have > a list of intramolecular interactions between atoms in a molecule within > the [ pairs ] section for which I believe gromacs generates the LJ C6 and > C12 values when the gen-pairs is set to yes. So I want to know if there is > any way to output/write the C6 and C12 values generated by gromacs to > screen/file. > gmx dump -s topol.tpr That will give you the processed topology, which includes c6 and c12. -- James "Wes" Barnett Postdoctoral Research Scientist Department of Chemical Engineering Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> Columbia University w.barn...@columbia.edu http://wbarnett.us -- 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] Domain Decomposition
On Wed, Nov 8, 2017 at 11:11 AM, Shraddha Parate <parateshrad...@gmail.com> wrote: > Dear Gromacs Users, > > I was able to achieve a spherical water droplet without periodic boundary > conditions (PBC) by changing few parameters in the .mdp files as below: > > However, I am facing the following error: > > *Fatal error:* > *Domain decomposition does not support simple neighbor searching, use grid > searching or run with one MPI rank.* > > I tried adding the '-nt 1' in the command for mdrun but it consumes 2 weeks > for a 1 ns simulation since it utilizes only 1 CPU. > > Is the error occurring because of changes in .mdp file parameters? Is there > any other way to make some changes in the mdrun command to make the > simulation faster? > > Thank you in advance. > > Best regards, > Shraddha Parate > The error indicates you should try changing how neighbor searching is done. Have you tried that? -- James "Wes" Barnett Postdoctoral Research Scientist Department of Chemical Engineering Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> Columbia University w.barn...@columbia.edu http://wbarnett.us -- 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] water molecule cannot be settled during minimization!!!!
On Mon, Nov 6, 2017 at 12:17 AM, Seera Suryanarayana <paluso...@gmail.com> wrote: > Dear gromacs users > > I am trying to simulate one protein with 180 residues. During energy > minimization I got the falling error. > > Fatal error: > > step 26: Water molecule starting at atom 28787 can not be settled. > Check for bad contacts and/or reduce the timestep if appropriate. > > I have reduced the em step size from 0.01 to 0.02 as I got this suggestion > from archives. I still have the same problem. I request you to give a > suggestion how to resolve it. > You went the wrong direction and increased the size of the time step, unless that is a typo. > > Thanks in advance > Surya > Graduate student > India. > -- James "Wes" Barnett Postdoctoral Research Scientist Department of Chemical Engineering Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> Columbia University w.barn...@columbia.edu http://wbarnett.us -- 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] angle/distance/position restraints in alchemical free energy calculation
On Fri, Nov 3, 2017 at 2:00 AM, minky son <minky0...@gmail.com> wrote: > Dear gmx user, > I’m studying about alchemical free energy calculation. > I have been read some articles about restraints during free energy > calculation, they referred the procedure in the article ( > http://pubs.acs.org/doi/pdf/10.1021/jp0217839). > I tried to search mailing list, but still I couldn’t understand. > I don't see any indication in that article of the researchers using GROMACS. It looks like they are using CHARMM. > The manual said “restraint-lambdas” option only handle dihedral > restraints, and the pull code restraints > How to apply angle/distance/position restraints with respect to lambda? > I don't believe those other restraints can be coupled for free energy changes in GROMACS at this time. -- James "Wes" Barnett Postdoctoral Research Scientist Department of Chemical Engineering Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> Columbia University w.barn...@columbia.edu http://wbarnett.us -- 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] Errant hydrogen bonds in the Lysozyme tutorial -- Please advise
On Sun, Oct 15, 2017 at 3:13 PM, Deron Johnson <der...@comcast.net> wrote: > BTW: I’m using > > gromacs 5.1.4 > VMD 1.9.3 > > on a Macbook Pro with macOS 10.12.3 (Sierra). > > > On Oct 15, 2017, at 12:08 PM, Deron Johnson <der...@comcast.net> wrote: > > > > I am new to gromacs. I followed the steps of the lysozyme tutorial > > (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > gmx-tutorials/lysozyme/01_pdb2gmx.html <http://www.bevanlab.biochem. > vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/01_pdb2gmx.html>) > > All the analysis checked out, so I believe I followed the steps > correctly. > > > > I then tried to visualize the results in VMD (by first loading npt.gro > and then loading > > md_0_1.xtc) I got a strange result: the hydrogen atoms for several water > molecules near > > the boundaries appear on the OTHER side of the box, and there are bonds > between these > > hydrogens and their associated oxygen molecules which stretch the entire > length of > > the box! (I've attached an image of the display window, using CPK > representation). > > > > Does anyone know how I can fix this? Did something get messed up during > solvation? > > > > > http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions > > -- > 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. -- James "Wes" Barnett Postdoctoral Research Scientist Department of Chemical Engineering Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> Columbia University w.barn...@columbia.edu http://wbarnett.us -- 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] Umbrella sampling: issue with COM distance far from initial value
On Tue, Oct 17, 2017 at 8:05 AM, Giuseppe Léonardo Licari < giuseppe.lic...@unige.ch> wrote: > Dear all, > > I have troubles with umbrella sampling. During the umbrella sampling > simulation the COM distance between the two solutes is going too far from > the set initial value. I tried to increase a lot the force constant of the > harmonic potential. I also tried to change "umbrella" to "contraint", with > no success. How can I fix the COM distance between the two solutes? It > seems that increasing the force constant does not work. Am I making some > mistake in the input? I have Gromacs v. 5.1.2 and here you can find the > files of a test simulation: > > https://www.dropbox.com/s/cl7au3twx8d6iip/test.zip?dl=0 > > As you see from the trajectory the two solutes go very far from the > initial COM distance. Does somebody have an idea about this? > > Thanks for the help and have a nice day. > Regards, > Licari > Giuseppe > I viewed the trajectory, but I can't see anything wrong. The two solutes seem to maintain a COM to COM distance that they started with. Note you are only doing the pull code on the z-vector so they are allowed to move as far as they want in the x and y directions from each other. Also your are using direction-periodic, which is probably not what you want. Use a bigger box, and use the distance method, or if you want to just do it along the z-vector (with direction, not direction-periodic) you will probably have to use a flat-bottom restraint to keep your solutes along the z-axis. -- James "Wes" Barnett Postdoctoral Research Scientist Department of Chemical Engineering Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> Columbia University w.barn...@columbia.edu http://wbarnett.us -- 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] Fwd: shift the LJ potential
On Wed, Oct 11, 2017 at 5:06 AM, Faezeh Pousaneh <fpoosa...@gmail.com> wrote: > Thank you Wes and Mark, > > Wes, that is what I am trying to do. However, still have problem. > I do not know how to derive sigma, epsilon (or C6 and C12) for my particle? > How the force fields have obtained C6 and C12 values in their .itp files > for each atom? > That depends on what the purpose of your simulation is. If you're just wanting a Lennard-Jones fluid, sigma=1.0 and epsilon=1.0 in reduced units could be reasonable. > > > Best regards > > > On Tue, Oct 10, 2017 at 7:55 PM, Wes Barnett <w.barn...@columbia.edu> > wrote: > >> On Tue, Oct 10, 2017 at 5:42 AM, Faezeh Pousaneh <fpoosa...@gmail.com> >> wrote: >> >> > Hi Mark >> > >> > I have a given function for pseudo hard-sphere potential, which has >> > different powers than LJ and a constant. I have to insert the constant >> in >> > order to properly define the cut-off for my hard spheres. >> > I just realized that I can use "user-specified potential". I guess I can >> > include the constant there, yes? >> > >> > One more thing, I need to have my own particles, spheres with a diameter >> > "a". How can I have them in gromacs? >> > . >> > >> >> This should get you started in generating your own tables: >> http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials >> >> If all you're looking to do is create repulsive spheres (again, not true >> hard spheres as Mark said; just removing attractions from the >> interactions), then cut off your interactions at 2^(1/6)*sigma and shift >> the potential at the cutoff to zero in your table. If you want different >> size spheres you need to subtract an additional term from r in the >> denominators of the c6 and c12 terms. >> >> -- >> James "Wes" Barnett >> Postdoctoral Research Scientist >> Department of Chemical Engineering >> Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> >> Columbia University >> w.barn...@columbia.edu >> http://wbarnett.us >> -- >> 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. >> > > -- James "Wes" Barnett Postdoctoral Research Scientist Department of Chemical Engineering Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> Columbia University w.barn...@columbia.edu http://wbarnett.us -- 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] Fwd: shift the LJ potential
On Tue, Oct 10, 2017 at 5:42 AM, Faezeh Pousaneh <fpoosa...@gmail.com> wrote: > Hi Mark > > I have a given function for pseudo hard-sphere potential, which has > different powers than LJ and a constant. I have to insert the constant in > order to properly define the cut-off for my hard spheres. > I just realized that I can use "user-specified potential". I guess I can > include the constant there, yes? > > One more thing, I need to have my own particles, spheres with a diameter > "a". How can I have them in gromacs? > . > This should get you started in generating your own tables: http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials If all you're looking to do is create repulsive spheres (again, not true hard spheres as Mark said; just removing attractions from the interactions), then cut off your interactions at 2^(1/6)*sigma and shift the potential at the cutoff to zero in your table. If you want different size spheres you need to subtract an additional term from r in the denominators of the c6 and c12 terms. -- James "Wes" Barnett Postdoctoral Research Scientist Department of Chemical Engineering Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> Columbia University w.barn...@columbia.edu http://wbarnett.us -- 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] manually adding non-bonded interactions based on atom number to topology file
eing any sign of attraction > > between monomer-monomer interfaces. > > > > [ nonbonded_params ] actually seems like the right place, since I've read > > that the parameters there *will* override the combination rules, but it > > looks like this section doesn't take atom numbers, but only atom types. > > Since I want these bonds to be based on site locations, this won't work. > Is > > there a way to specify non-bonded parameters using atom numbers? > > > > Any clarification you can provide will be helpful. > > > > Before delving into this too much, to clarify: you want to simulate a > polymer melt with some modified interactions between the ends of each > polymer? > > -- > James "Wes" Barnett > Postdoctoral Research Scientist > Department of Chemical Engineering > Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> > Columbia University > w.barn...@columbia.edu > http://wbarnett.us > > > > Hi, > > First, You must need a very long simulation box because one monomer's > length exceed the cut-off. > > I don't think only LJ can naturely make monomers linear polymer. I know you > need acceleration of one monomer's A end binding to the other's B end. So I > will recommend the PLUMED to add some far-large-near-small restraints > between A and B end of different monomers. > > Cheers, > Yu > -- > 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. > -- James "Wes" Barnett Postdoctoral Research Scientist Department of Chemical Engineering Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> Columbia University w.barn...@columbia.edu http://wbarnett.us -- 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] manually adding non-bonded interactions based on atom number to topology file
On Wed, Sep 27, 2017 at 8:07 PM, Amanda Parker <aspar...@ucdavis.edu> wrote: > Hello, > > I am trying to create my own topology file in order to simulate assembly of > a number of identical monomers. I have been reading the manual, mailing > list, and other online sources, about what all the sections in the topology > mean and how to construct them, but I'm still confused about what is > necessary and what overrides what. > > I would like to be able to have any number of monomers in my system and > therefore I want all the intermolecular interactions to be non-specific. I > want each monomer to have atom numbers running from 1 to last_atom_number, > so that I can have atom 1 paired with atom last_atom_number, and see > binding between any monomer's atom 1 with any other monomer's atom > last_atom_number. > > So my idea is to create a single topology file, which will contain the > intramolecular interactions for a single monomer, as well as the > interactions between atom 1 and atom last_atom_number. The latter will > probably be Lennard-Jones interactions, since that way the "beginning" of > one monomer will not interact with its own "end" (due to the cut-off), but > with other monomers' ends if they get close enough. I'd like to manually > adjust the parameters for these interactions, to accelerate binding. > > The problem is that I don't know where to put these Lennard Jones > interactions. > > Right now I have them in the [ pairs ] section, since my understanding is > that this is where one can put "extra" non-bonded interactions with special > parameters. But it also seems like this depends on the force field and that > sometimes [ pairs ] should only be for a list of 1-4 interactions. Since > I'm writing my own topology (not using pdb2gmx), what will [ pairs ] > specify? Will the parameters in [ pairs ] override the parameters in [ > atomtypes ]? I have increased the c6 parameter and decreased the c12 > parameter considerably, and I'm still not seeing any sign of attraction > between monomer-monomer interfaces. > > [ nonbonded_params ] actually seems like the right place, since I've read > that the parameters there *will* override the combination rules, but it > looks like this section doesn't take atom numbers, but only atom types. > Since I want these bonds to be based on site locations, this won't work. Is > there a way to specify non-bonded parameters using atom numbers? > > Any clarification you can provide will be helpful. > Before delving into this too much, to clarify: you want to simulate a polymer melt with some modified interactions between the ends of each polymer? -- James "Wes" Barnett Postdoctoral Research Scientist Department of Chemical Engineering Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> Columbia University w.barn...@columbia.edu http://wbarnett.us -- 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] compilation of gromacs 2016.3 or 4 with C compiler flag -fdebug-prefix-map=/build/gromacs-GTZ9iZ/gromacs-2016.1=.
assed : > here an extract of the output > -- > 89% tests passed, 3 tests failed out of 27 > > Label Time Summary: > GTest = 2.77 sec (18 tests) > IntegrationTest = 0.32 sec (2 tests) > MpiIntegrationTest= 0.13 sec (1 test) > UnitTest = 2.77 sec (18 tests) > > Total Test time (real) = 198.07 sec > > The following tests FAILED: > 15 - GmxPreprocessTests (Failed) > 20 - MdrunTests (Failed) > 21 - MdrunMpiTests (Failed) > > > > > 3) when using mdrun, at the end of an md, for example, in a basic > test, I see an undefined symbol error : > > The end of the output : > > starting mdrun 'DSPC BILAYER' > 4000 steps,100.0 ps. > > step 40 Turning on dynamic load balancing, because the performance loss > due to load imbalance is 4.1 %. > > > step 3600 Turning off dynamic load balancing, because it is degrading > performance. > > > Writing final coordinates. > /home/cloison/Softwares/GROMACS2016/bin/gmx: symbol lookup > error: /home/cloison/Softwares/GROMACS2016/bin/gmx: undefined symbol: > walltime_accounting_set_valid_finish > > > The usual performance report is absent. > > As far as I understand, in the code, the function > walltime_accounting_set_valid_finish > is defined in gromacs2016.3, but not in 2016.1, > so I have the impression that I get a mixture of the two versions !? > > > It looks like to me you also have 2016.1 installed and are calling that one. You specified "/home/cloison/Softwares/GROMACS2016/gromacs-2016.3" as the installation path for 2016.3, but gmx shows to be located at ' /home/cloison/Softwares/GROMACS2016/gromacs-2016.3/gromacs-2016.3/build_ilmfixe160/./bin/gmx', which is not what you specified. Additionally the error is saying gmx is located "/home/cloison/Softwares/GROMACS2016/bin/gmx", which again is not what you specified. Ensure that you build in a clean, empty directory, and also install to an empty directory. Then make sure PATH is correctly set. -- James "Wes" Barnett Postdoctoral Research Scientist Department of Chemical Engineering Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> Columbia University w.barn...@columbia.edu http://wbarnett.us -- 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] Molecule leave from the simulation box
On Wed, Sep 20, 2017 at 11:53 PM, Sameer Edirisinghe <noot...@gmail.com> wrote: > Dear Users, > > I have done simulation for polymer system which is having 20 molecules. But > after nvt equilibrium 2 molecules leave the simulation box. Is this > affecting to my production run or analysis? > > Is it possible to re-center all molecules? > > http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions -- James "Wes" Barnett Postdoctoral Research Scientist Department of Chemical Engineering Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> Columbia University w.barn...@columbia.edu http://wbarnett.us -- 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] Free Energy Calculations: Error during minimization step.
= 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 > > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 > > 0.00 0.00 > > restraint_lambdas= 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 > > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 > > 0.00 0.00 > > mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 > > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 > > 0.00 0.00 > > temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 > > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 > > 0.00 0.00 > > ; Options for the decoupling > > sc-alpha = 0.5 > > sc-coul = no ; linear interpolation of Coulomb > > (none in this case) > > sc-power = 1 > > sc-sigma = 0.3 > > couple-moltype = Protein ; name of moleculetype to decouple > > couple-lambda0 = vdw-q > > couple-lambda1 = none > > couple-intramol = no > > nstdhdl = 10 > > > > > > > > > > > > As you can see, I want to first annihilate the charges, followed by a vdw > > tranformation, using a total of 41 lambdas. Since both charges and vdw > are > > being interpolated, the topology files contain the normal charges for the > > transformed molecule. This setup is similar to what Wes had suggested in > a > > previous response to this thread. > > > > The issue is that I am facing the exactly the same error in minimization > > step at final lambda state where both vdw and electrostatics are turned > off. > > > > > > > > -- > > Program gmx mdrun, VERSION 5.1.2 > > Source code file: /home/bp-lab/Downloads/gromacs-5.1.2/src/gromacs/ > mdlib/constr.cpp, > > line: 555 > > > > Fatal error: > > > > step 10: Water molecule starting at atom 120 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > > > For more information and tips for troubleshooting, please check the > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > > > > > > > --- > > > > Now, what I understood is that in case of just the vdw transformation, > > since we are not calculating any electrostatics, the charges should be > zero > > in topology file. Whereas, in case of just the charge transformation, the > > charges are required in the topology file as charges are interpolated in > > this step. And performing the simulation as such give no errors. > > > > I do not understand why the error is surfacing in case of a [vdw-q] to > > [none ] tranformation., especially now that the charges are gradually > > decoupled prior to decoupling the vdw interactions. Any help will be > > greatly appreciated. > > > > Sincerely, > > Abhishek > > > > > > Abhishek Acharya > > Research Associate, > > Department of Molecular Nutrition > > CSIR-Central Food Technological Research Institute, > > Mysuru-570020 > > > > On Sun, Sep 10, 2017 at 8:02 AM, Abhishek Acharya < > > abhi117acha...@gmail.com> wrote: > > > >> > >> > >> > >> You can do them separately, but the charges need to have been turned off > >> for the molecule you are transforming for the second step when turning > off > >> vdw. In other words, all charges must be 0.0 for the molecule in the > >> topology file for the vdw transformation. Is that what you've done? > >> > >> Justin's tutorial gives an explanation on why this needs to be done, and > >> in > >
Re: [gmx-users] gromacs error
On Mon, Sep 11, 2017 at 8:44 AM, Vidya R <vidyadevi2...@gmail.com> wrote: > Hi, > > > When I give these two commands > > gmx grompp -f mdp/min.mdp -o min -pp min -po min > gmx mdrun -deffnm min > > I get this error. > > What to do? > > > > Reading file min.tpr, VERSION 5.0.2 (single precision) > tMPI error: tMPI Initialization error (in valid comm) > > Thanks, > Vidya.R > I can't speak to that exact error, but there have been several bug fix releases to the 5.0.x series since 5.0.2, so an upgrade may be in order. I would even suggest upgrading to the latest release (2016.x series). -- James "Wes" Barnett Postdoctoral Research Scientist Department of Chemical Engineering Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> Columbia University w.barn...@columbia.edu http://wbarnett.us -- 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] Free Energy Calculations: Error during minimization step.
On Sat, Sep 9, 2017 at 10:10 AM, Abhishek Acharya <abhi117acha...@gmail.com> wrote: > Hello Wes, > > Thanks for your reply. > > Sorry, I did not understand why we need to turn off charges first and then > vdw, if the are performing both steps separately. > > I was attempting to perform the vdw and charge transformations separately. > So for the vdw transformation, if I use c-lambda0=vdw > and c-lambda1=none, I think that would signal gromacs that the > electrostatics are turned off at all lambda values.and the vdw interpolate > from full strength at lambda=0 to none at lambda=1.0 > You can do them separately, but the charges need to have been turned off for the molecule you are transforming for the second step when turning off vdw. In other words, all charges must be 0.0 for the molecule in the topology file for the vdw transformation. Is that what you've done? Justin's tutorial gives an explanation on why this needs to be done, and in his topology he had all charges at 0.0 in the methane topology file. -- James "Wes" Barnett Postdoctoral Research Scientist Department of Chemical Engineering Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> Columbia University w.barn...@columbia.edu http://wbarnett.us -- 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] Free Energy Calculations: Error during minimization step.
> Intriguingly, I this case I got the exact error as above, but this time at > lambda=0. > That make sense, since in both cases the vdw interactions are off in both situations (couple-lambda0 or couple-lambda1 = none). > --- > Program gmx mdrun, VERSION 5.1.2 > Source code file: > /home/bp-lab/Downloads/gromacs-5.1.2/src/gromacs/mdlib/constr.cpp, line: > 555 > > Fatal error: > > step 10: Water molecule starting at atom 120 can not be settled. > Check for bad contacts and/or reduce the timestep if appropriate. > > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > --- > > LINCS has been used to constrain all-bonds with lincs_order = 12. > > Analysis of step10b.pdb and step10c.pdb did not reveal any obvious clashes > between water molecules. > > I have also run simulations for charge annihilation step and I did not face > such a problem. > Has the charge been turned off for this series of simulations? You should generally turn electrostatics off through a series of free energy simulations and then turn off VDW while the charge is off. > > Looking for the some advice on how to proceed from here. > I do something like this: vdw-lambdas = 0.00 0.00 0.00 0.00 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00 coul-lambdas = 0.00 0.25 0.50 0.75 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 couple-lambda0 = vdw-q couple-lambda1 = none See: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html http://wbarnett.us/tutorials/4_methane_fe/ -- James "Wes" Barnett Postdoctoral Research Scientist Department of Chemical Engineering Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> Columbia University w.barn...@columbia.edu http://wbarnett.us -- 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] Running multiple Gromacs simulations on the same node
On Fri, Sep 8, 2017 at 12:00 AM, MING HA <ming...@scarletmail.rutgers.edu> wrote: > Hi all, > > > It may seem a bit weird, but I'm trying to run multiple Gromacs simulations > simultaneously on the same node, and I specified each Gromacs simulation > to use only 1 MPI process and 1 OMP thread. I'm doing this because I am > trying to check how accurate my model can predict an application using a > single thread and process. > > My question is: If, for example, I am running multiple Gromacs simulations > simultaneously, each with 1 MPI process and 1 OMP thread, on the same > node, does each simulation use separate MPI processes and OMP threads, > or are they shared? > > > Sincerely, > Ming I think that depends on how your mpi library decides to assign threads. I know there are some switches that you can pass to mpirun that modify this behavior. mdrun also has the "-pin on" setting that can prevent threads from moving around. See http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Pinning_threads_to_physical_cores You could also try using the "-multi" and "-multidir" flags provided by mdrun to run multiple simulations at the same time with one mdrun command. -- James "Wes" Barnett Postdoctoral Research Scientist Department of Chemical Engineering Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> Columbia University w.barn...@columbia.edu http://wbarnett.us -- 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] gromacs installation
On Thu, Sep 7, 2017 at 3:25 PM, vijayakumar gosu <vijayakumarg...@gmail.com> wrote: > Hi, > > I have installed gromacs 5.1 in server which has 4 nodes each with 40 cpus. > I am allotted to use only 2 nodes with 80 cpus. after installation when i > did sample md run only 20 cpus are being utilized. How can I fully utilize > the all 80 CPUs for mdrun. > > I have used below cmake command for the installation > > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=OFF > -DREGRESSIONTEST_PATH=/BiO/BioTools/regressiontests-5.1.1 -DGMX_GPU=ON > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda > -DCMAKE_INSTALL_PREFIX=/Bio/BioTools/gromacs > > I have not seen any errors during installation. > You should go ahead and just install 2016.3 instead of 5.1. What is your exact command when you run mdrun? -- James "Wes" Barnett Postdoctoral Research Scientist Department of Chemical Engineering Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> Columbia University w.barn...@columbia.edu http://wbarnett.us -- 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] successive removal of position restrain?
On Wed, Sep 6, 2017 at 5:36 AM, Seera Suryanarayana <paluso...@gmail.com> wrote: > Dear gromacs users, > > I have gone through one gromacs tutorial of md simulation in solvent. Where > they mentioned that successive removal of position restrain. In other words > first they have done NPT ensemble with 1000 1000 1000 energy constants, > then re executed the NPT ensemble with 100 100 100 energy constants and > finally third time they ran the NPT ensemble with 10 10 10 energy > constants. After this run they have stated the real MD production run with > position restraint. But I have done NPT ensemble only with 1000 1000 1000 > force constant and then I removed the complete position restrains before MD > production run. My question comes here, Is there any difference between > their methodology and my methodology? > > Thanks in advance > Surya > Graduate student > India. > Hard to know since we don't know what your system is or why you are using position restraints and then removing them. Have you contacted the author of the tutorial? -- James "Wes" Barnett Postdoctoral Research Scientist Department of Chemical Engineering Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> Columbia University w.barn...@columbia.edu http://wbarnett.us -- 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] GPU-accelerated performance
On Wed, Sep 6, 2017 at 4:58 AM, Alex <nedoma...@gmail.com> wrote: > Hi all, > > We just got the new machines that were actually built with Szilárd's > advice (a while back) and I am doing some preliminary tests. "My" machine > has two 22-core Xeon E5 CPUs (44 cores / 88 threads total) + 3 Titan Xp > GPUs. So far, I got good test system performance (~11K atoms, 92 ns/day) > from '-nt 36' and running on all GPUs. Further increasing the number of > threads only reduces performance. The test system is a CHARMM-based > lipid+water setup, elongated in the Z-direction (6.7 nm x 6.7 nm x 11.2 > nm).Very decent performance (70 ns/day) for 16 CPU cores and two GPUs. > > Any suggestions on further increase what we can squeeze out of this thing > for a single simulation? The relevant mdp section is below (CHARMM > defaults, really). What would you try in your mdrun line? > > Thanks! > > Alex > > > cutoff-scheme = Verlet > nstlist = 20 > rlist = 1.2 > coulombtype = pme > rcoulomb= 1.2 > vdwtype = Cut-off > vdw-modifier= Force-switch > rvdw_switch = 1.0 > rvdw= 1.2 > > You really just have to try different options for different systems. The performance will be system-dependent. Expect larger systems to benefit more from GPU acceleration. Try different combinations of MPI ranks and OMP threads along with specifying the GPU's multiple times. I always do a series of short runs with different combinations before choosing the fastest one for a particular system and then doing a longer production run. See http://www.gromacs.org/Documentation/Acceleration_and_parallelization -- James "Wes" Barnett Postdoctoral Research Scientist Department of Chemical Engineering Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> Columbia University w.barn...@columbia.edu http://wbarnett.us -- 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] Using "gmx msd"
> I went through your tutorial and it is very helpful for beginners like me. > > You have discussed "one methane in water" to calculate RDF... > > Can we follow the same procedure to compute the diffusion co-efficient of > methane at the end of the production MD, using gmx msd instead of gmx rdf? > > Or should we change the parameters to calculate MSD? > Hi Vidya, I have cc'd the GROMACS mailing list. After the simulation you need to postprocess your xtc file so that it is "unwrapped"; otherwise, your msd will be artificially low, since the methane molecule will have gone across the peridiodic boundary condition several times. I believe you need to use "gmx trjconv" with the "-pbc nojump" option. Then you can run "gmx msd" on the new xtc file. See "man gmx-trjconv" for more information on how to use the "nojump" option. -- James "Wes" Barnett Postdoctoral Research Scientist Department of Chemical Engineering Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> Columbia University w.barn...@columbia.edu http://wbarnett.us -- 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.
