[gmx-users] Performing energy minimisation for an alanine scan
I'm trying to minimise 600+ structure. They differ by an alanine substitution, which has been put in place using stateA/stateB topologies. The technique used to generate the initial structure was taken from: http://pmx.mpibpc.mpg.de/output.pl?jobid=model_scanA_amber99sb-star-ildn-mut.ff_3329_20180703151957 This produces a topology of: stateA -> wildtype amino acid stateB -> alanine substitution Given the number of structures, I am trying to automate everything. Centering, solvating, genion etc., all done. Now I come to an initial energy minimisation for each structure. Unfortunately, emtol is aren't falling < 1000, which I find to be a value sufficient to move on from energy minimisation to more dynamical equilibrium methodologies. One could argue that I should look at the trajectory, but I want the parameters correct first, especially given how I am automating this. Since the alanine scan methodology generated stateA/stateB topologies per structure, I figured that I need to use free energy parameters in my .mdp file to ensure that I am immediately only ever using the stateB (alanine) topology. I basically need someone to sanity check the .mdp values to ensure that I only use stateB (the alanine topology) during the energy minimisation. The complete free energy .mdp values (from the mdout.mdp) file are: ; Free energy variables free-energy = yes couple-moltype = couple-lambda0 = vdw-q couple-lambda1 = vdw-q couple-intramol = no init-lambda = -1 init-lambda-state= 0 delta-lambda = 0 nstdhdl = 10 fep-lambdas = mass-lambdas = coul-lambdas = 1.0 vdw-lambdas = 1.0 bonded-lambdas = 1.0 restraint-lambdas= 1.0 temperature-lambdas = calc-lambda-neighbors= 1 init-lambda-weights = dhdl-print-energy= no sc-alpha = 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 Please note, key-value pairs like coul-lambdas and vdw-lambdas are 1.0 as I only want to model state B and I am not interested in slow growth. Are these parameters sufficient for modelling stateB upon immediate execution of an energy minimisation (and NPT/NVT dynamics)? I've had very little experience with the lambda implementation in gromacs and I turn to more experience. Many thanks Anthony Kind regards Anthony Nash PhD MRSC Department of Physiology, Anatomy, and Genetics University of Oxford -- 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 get the complete molecule?
try "-pbc whole" instead of "-pbc mol" El sáb., 7 jul. 2018 a las 2:13, Anjana Jayasinghe () escribió: > Dear All, > In my simulation, part of my molecule is in a one cell and the other part > is in the adjacent cell. I want to get the complete molecule in the pdb > format in the center of the box. I tried to do that using gmx trjconv -f > run.pdb -s run.tpr -pbc mol -ur compact -center -o run_new.pdbBut I > couldn't get what I want. Can anyone help me? > 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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] building GROMACS 2018.2
May wish to use ccmake and check correct links to Cuda are done. On 07/07/2018 08:11 PM, Sevahn Kayaneh Vorperian wrote: Dear All, I am new to GROMACS and wanted to build the 2018.2 version so that I can do some MD work. I am following the instructions under "Quick and Dirty Installation" verbatim: http://manual.gromacs.org/documentation/2018/install-guide/index.html I got the latest version of CUDA and CMAKE. I didn't bother with MPI support since I'm not running on multiple networks. For FFT, I did the following during the cmake step to acquire it cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON this went fine, as well as the make command however, during make check, I got an error at 97% (where terminal said: Linking CXX shared library ../../../../lib/libgpu_utilstest_cuda.dylib); attaching the output I got here. I ran the commands in the folder I made called build-gromacs not build; that was the only difference from the documentation in the manual, but the correct folders were referenced, so it shouldn’t be a problem. I'm unsure how to proceed from here, and what adjustments I need to make so that I can finish building GROMACS. Would really appreciate guidance… I saw previous problems posted on the site where people got stuck at 2 or 3% during the build with similar terminal output with it crashed, but the resolution for how to get past this was unclear. Thanks! Sevahn -- 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] Force field parameter
I have already mailed them... waiting for their reply.. On Sat, 7 Jul 2018, 11:22 pm Mark Abraham, wrote: > Hi, > > Your other good approach is to contact the authors to ask them to share > their methodology fully, ie force field files. > > Mark > > On Sat, Jul 7, 2018, 13:47 Soham Sarkar wrote: > > > Dear All, > > Can anyone please tell me, where from I get the parameters > for > > Osmotic, Kast, Netz force field like the files OPLS, CHARMM which is > > already in GROMACS? I have got the files for the KBFF force field but not > > these three. The paper by Dias and group > > https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.119.108102 > used > > different force field. I want to go that way.Please provide me with the > > links or relevant websites for the filese regarding the force field. > Thanks > > in advance. > > -Soham > > > > -- > > SOHAM SARKAR > > Junior Research Fellow > > Department of Chemistry > > INDIAN INSTITUTE OF TECHNOLOGY BOMBAY > > -- > > 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] building GROMACS 2018.2
Dear All, I am new to GROMACS and wanted to build the 2018.2 version so that I can do some MD work. I am following the instructions under "Quick and Dirty Installation" verbatim: http://manual.gromacs.org/documentation/2018/install-guide/index.html I got the latest version of CUDA and CMAKE. I didn't bother with MPI support since I'm not running on multiple networks. For FFT, I did the following during the cmake step to acquire it cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON this went fine, as well as the make command however, during make check, I got an error at 97% (where terminal said: Linking CXX shared library ../../../../lib/libgpu_utilstest_cuda.dylib); attaching the output I got here. I ran the commands in the folder I made called build-gromacs not build; that was the only difference from the documentation in the manual, but the correct folders were referenced, so it shouldn’t be a problem. I'm unsure how to proceed from here, and what adjustments I need to make so that I can finish building GROMACS. Would really appreciate guidance… I saw previous problems posted on the site where people got stuck at 2 or 3% during the build with similar terminal output with it crashed, but the resolution for how to get past this was unclear. Thanks! Sevahn -- 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] Force field parameter
Hi, Your other good approach is to contact the authors to ask them to share their methodology fully, ie force field files. Mark On Sat, Jul 7, 2018, 13:47 Soham Sarkar wrote: > Dear All, > Can anyone please tell me, where from I get the parameters for > Osmotic, Kast, Netz force field like the files OPLS, CHARMM which is > already in GROMACS? I have got the files for the KBFF force field but not > these three. The paper by Dias and group > https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.119.108102 used > different force field. I want to go that way.Please provide me with the > links or relevant websites for the filese regarding the force field. Thanks > in advance. > -Soham > > -- > SOHAM SARKAR > Junior Research Fellow > Department of Chemistry > INDIAN INSTITUTE OF TECHNOLOGY BOMBAY > -- > 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] How to get the complete molecule?
Dear All, In my simulation, part of my molecule is in a one cell and the other part is in the adjacent cell. I want to get the complete molecule in the pdb format in the center of the box. I tried to do that using gmx trjconv -f run.pdb -s run.tpr -pbc mol -ur compact -center -o run_new.pdbBut I couldn't get what I want. Can anyone help me? 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.
