[gmx-users] simulation settings
Dear Gromacs users and developers, I want to perform simulation of peptide dissolved in water using NPT. For constant temperature I use Berendsen temperature coupling. Do I have to define tc-grps for 2 groups (protein and solvent) or I may use tc-grps =System. What is the difference? The person who introduced gromacs to me uses tc-grps = Protein Sol_Ions but he is not sure why it should be in this way if at all Can you, please elucidate this issue to me. Thank you a lot. Regina This message was sent using IMP, the Internet Messaging Program. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] simulation settings
On 1/03/2010 12:00 AM, pol...@fh.huji.ac.il wrote: Dear Gromacs users and developers, I want to perform simulation of peptide dissolved in water using NPT. For constant temperature I use Berendsen temperature coupling. Do I have to define tc-grps for 2 groups (protein and solvent) or I may use tc-grps =System. What is the difference? The person who introduced gromacs to me uses tc-grps = Protein Sol_Ions but he is not sure why it should be in this way if at all Can you, please elucidate this issue to me. There's some quick advice here http://www.gromacs.org/Documentation/Terminology/Thermostats, otherwise consult some textbook material. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Question about distance restraints, energy minimization and time averaging.
Hi, all, This is probably a very simple question. Does time averaging apply, when distance restraints are used during energy minimization (steepest descent or conjugate gradient)? Your input would be greatly appreciated. Art Roberts Dr. Arthur Roberts, Ph.D. University of California, San Diego Skaggs School of Pharmacy and Pharmaceutical Sciences 9500 Gilman Drive #0703 La Jolla, CA 92093-0703 email: aroberts99...@yahoo.com cell: 206-850-7468 skype=aroberts92122 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Question about distance restraints, energy minimization and time averaging.
Hi, I'm not sure if I understand exactly what you meen, but since there's no time propagation during energy minimization, time-averages don't make much sense. Erik Arthur Roberts skrev: Hi, all, This is probably a very simple question. Does time averaging apply, when distance restraints are used during energy minimization (steepest descent or conjugate gradient)? Your input would be greatly appreciated. Art Roberts Dr. Arthur Roberts, Ph.D. University of California, San Diego Skaggs School of Pharmacy and Pharmaceutical Sciences 9500 Gilman Drive #0703 La Jolla, CA 92093-0703 email: aroberts99...@yahoo.com cell: 206-850-7468 skype=aroberts92122 -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] NVE of water
Dear users, for test purposes in order to set up a bigger system, I try to run NVE simulations of SPC water, but the energy increases very rapidely. My guess is that the cutoffs I use are not good for water. I that the case ( I would be grateful for a good reference for suitable SPC water parameters) or do I miss something else? My parameter file for the NVE is: title= NVE cpp = /lib/cpp integrator = md dt = 0.002 ; ps ! = 2 fs nsteps = 5 ; total 100 ps nstxout = 5000 nstvout = 5000 nstxtcout= 0 nstlog = 5000 nstenergy= 5000 nstlist = 10 ns_type = grid rlist= 1.1 unconstrained-start = yes constraints = all-bonds constraint_algorithm = shake shake_tol= 0.0001 ;VdW vdwtype = Switch rvdw = 1.0 ; rvdw+ (0.1:0.3)= rlist rvdw_switch = 0.9 gen_vel = no ; yes gen_temp = 300 gen_seed = -1 ;Temperature coupling tc_grps = system tcoupl = no ;nose-hoover tau_t= 0.1 ref_t= 300 ;Pressure coupling pcoupl = no optimize_fft = yes Any suggesions are really welcome. Thank you. Regards, Andrea Muntean -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Anisotropic pressure control
Why is it that what you have run with xy rigid and z couple not correct? Fluctuating box volume is exactly what you would expect to get, and do get, with pressure coupling. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Matteus Lindgren Sent: Friday, 26 February 2010 8:24 PM To: gmx-users@gromacs.org Subject: [gmx-users] Anisotropic pressure control Dear experts, I am trying to run MD on a protein in water above a flat surface of TiO2 in a cubic box with pressure control. All the atoms of TiO2 are frozen and I therefore think that anisotropic pressure control must be used. I tried allowing box fluctuations in the direction of the normal vector (the z-axis) of the TiO2 surface but the box volume then oscillates during the whole simulation. The same parameters worked for a simulation of protein+water without the frozen TiO2 surface. How can I use pressure control for a system with a frozen surface that extends through the whole box? Ive read the posts about membrane simulations but membranes are flexible so I think those suggestions might not apply. The important part of the input file was as follows: nstlist = 10 ns_type = grid pbc = xyz periodic_molecules = no rlist= 1.2 coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.2 epsilon-r= 1 epsilon_rf = 1 vdw-type = Cut-off rvdw-switch = 0 rvdw = 1.4 DispCorr = EnerPres table-extension = 1.5 energygrp_table = fourierspacing = 0.12 pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d optimize_fft = yes Tcoupl = Nose-hoover tc-grps = protres RUT solcl tau_t= 0.1 0.1 0.1 ref_t= 310 310 310 Pcoupl = Parrinello-Rahman Pcoupltype = anisotropic tau_p= 2.0 2.0 2.0 2.0 2.0 2.0 compressibility = 0.0 0.0 5e-5 0.0 0.0 0.0 ref_p= 0 0 1.01325 0 0 0 gen_vel = yes gen_temp = 310 gen_seed = 1993 constraints = hbonds constraint-algorithm = lincs continuation = yes lincs-order = 4 lincs-iter = 4 freezegrps = frozen freezedim= Y Y Y Thanks Matteus - Matteus Lindgren, graduate student Department of Chemistry, Umeå University SE-901 87 Umeå, Sweden Phone: +46 (0)90-7865368 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Position restrained dynamics crash
Dear All, I am trying to do position restrained dynamics of a protein with co-factor in Gromacs Version 4. But after running for a while (1390 steps), the run is simply stopping. I am not getting any message on log file or terminal. Please help to identify the problem. This is my pr.mdp file parameters: ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; title = Yo cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 15000; total 30 ps. nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft= yes ; temperature coupling is on in two groups Tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 ; Pressure coupling is on Pcoupl = Parrinello-Rahman Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 Thank You, Regards, Sukesh. -- Sukesh Chandra Gain TCS Innovation Labs Tata Consultancy Services Ltd. 'Deccan Park', Madhapur Hyderabad 500081 Phone: +91 40 6667 3572 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Please help me with ACPYPI
Dear All, I would like to ask for your help to my problem dealing with making topology file for ligand with OPLS-AA forcefield by following TutorialAcpypi4GromacsOPLS. Now, let me show you my steps: - Getting my ligand.pdb file from PDB - Adding all hydrogen by PRODRG2.5 Server with GROMOS 87 forcefield, full charges, no EM, full chirality - Using antechamber to convert ligand.pdb to ligand_bcc.pdb (antechamber -i ligand.pdb -fi pdb -o ligand_bcc.pdb -fo pdb -c bcc) - Running ACPYPI (acpypi -i ligand_bcc.pdb), then obtaining folder ligand_bcc.acpypi, including my wanted file: ligand_bcc_GMX_OPLS.itp. However, some problems occured: 17 opls_x 1 MOL O24 17-0.447600 0.0 ; qtot -0.186 x 22 opls_x 1 MOLC4 22-0.147400 0.0 ; qtot -0.168 x It seems that OPLS-AA forcefield does not recognize what Amber forcefield have assigned for this atomtype/bondtype. Then, it stopped me there from running the next steps in order to perform modeling dynamics simulation of protein-ligand complex in Gromacs with OPLS-AA forcefield. Could you please help me to solve this problem? I really hope to hear from you soon! Thanks in advances! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_sas
*I executed the following command. ** **g_sas -s mdrun.tpr -f mdrun.trr -or mdrun.xvg *** ** *xmgrace -nxy mdrun.xvg* *I get two sets of values: one is bigger (black) than the other (red). *** *I have checked the manual and other sources, but I could not find an **answer about the black and red line. If it was written in fine print and I missed it, I am sorry **about that. So I want to know is the red lower value, the standard error or standard deviation or something else? What does red and black line shows also link the reference.* -- Pawan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Constraining periodic cell
Dear All, We are running some simulations using an anisotropic periodic cell. We are getting 'cell runaway' with the cell becoming very long and thin. This appears to being driven by the electrostatics of the system. The simulation then dies because the smallest cell dimension is less than 2*cutoff. Is there a way that we can apply some constraints to the periodic cell? Regards David David Chalmers Lab: 9903 9110 Senior Lecturer Fax: 9903 9582 Faculty of Pharmacy and Pharmaceutical Sciences Monash University 381 Royal Pde, Parkville, Vic 3053. Australia -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Constraining periodic cell
On 2010-03-01 07.27, David Chalmers wrote: Dear All, We are running some simulations using an anisotropic periodic cell. We are getting 'cell runaway' with the cell becoming very long and thin. This appears to being driven by the electrostatics of the system. The simulation then dies because the smallest cell dimension is less than 2*cutoff. Is there a way that we can apply some constraints to the periodic cell? Why not use isotropic pressure coupling? Regards David David Chalmers Lab: 9903 9110 Senior Lecturer Fax: 9903 9582 Faculty of Pharmacy and Pharmaceutical Sciences Monash University 381 Royal Pde, Parkville, Vic 3053. Australia -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_sas
Hi Pawan, The legends are contained in the .xvg file. Try viewing the file. Cheers, Tsjerk On Mon, Mar 1, 2010 at 8:29 AM, pawan raghav pwnr...@gmail.com wrote: I executed the following command. g_sas -s mdrun.tpr -f mdrun.trr -or mdrun.xvg xmgrace -nxy mdrun.xvg I get two sets of values: one is bigger (black) than the other (red). I have checked the manual and other sources, but I could not find an answer about the black and red line. If it was written in fine print and I missed it, I am sorry about that. So I want to know is the red lower value, the standard error or standard deviation or something else? What does red and black line shows also link the reference. -- Pawan -- gmx-users mailing list gmx-us...@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_sas
On 1/03/2010 6:29 PM, pawan raghav wrote: /I executed the following command. // //g_sas -s mdrun.tpr -f mdrun.trr -or mdrun.xvg /// // /xmgrace -nxy mdrun.xvg/ /I get two sets of values: one is bigger (black) than the other (red). /// /I have checked the manual and other sources, but I could not find an //answer about the black and red line. If it was written in fine print and I missed it, I am sorry //about that. So I want to know is the red lower value, the standard error or standard deviation or /something else? What does red and black line shows also link the reference.// Look in the .xvg file for the headings for the data sets s0, s1, etc. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
