[gmx-users] Ligand charge issues
Hi Gromacs users, I am studying the protein-ligand interaction using amber99sb-ILDN force field in gromacs 4.6.2. To create the ligand topology (lipid A), I have used online version of ACPYPE/antechamber.http://webapps.ccpn.ac.uk/acpype/ I have read a lot more time that charge on different atoms are not correct when created through various softwares/scripts. My question is whether ACPYPE/antechamber also fall in this category? If yes, can anyone please provide me with any link from where I can get charge values to assign? Thank you.mayaz -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] mdp file help
Hi guys, I'm new to Gromacs and seeking some input on my .mdp file for the production run. I want to perform simulation to check protein stability over time and the after that the stable protein will be used for protein-protein docking/interactions. I'm using cubic box (with 1nm pbc) with water and Cl ions to neutralize on a GPU accelerated system. my mdp file is as: title = Protein in water ; Run parameters integrator = md ; leap-frog integrator nsteps = 2000 ; 2 * 50 = 1000 ps, 1 ns dt = 0.002 ; 2 fs cutoff-scheme = Verlet ; for GPU acceleration verlet-buffer-drift = -1 ; now use nstlist ; Output control nstxout = 1000 ; save coordinates every 2 ps nstvout = 1000 ; save velocities every 2 ps nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps nstenergy= 1000 ; save energies every 2 ps nstlog = 1000 ; update log file every 2 ps ; Bond parameters continuation= yes; Restarting after NPT constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order= 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist= 30 ; 10 fs rlist = 0.6; short-range neighborlist cutoff (in nm) rcoulomb = 0.6 ; short-range electrostatic cutoff (in nm) rvdw= 0.6 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4; cubic interpolation fourierspacing= 0.12 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p= 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off By performing a test run with ff99SB force field, I got an efficiency as follow: Reading file test11.tpr, VERSION 4.6.1 (single precision) Using 1 MPI thread Using 4 OpenMP threads 1 GPU detected: #0: NVIDIA GeForce GT 630, compute cap.: 3.0, ECC: no, stat: compatible 1 GPU auto-selected for this run: #0 starting mdrun 'Protein in water' 2000 steps, 4.0 ps. step 60: timed with pme grid 104 104 104, coulomb cutoff 0.600: 6760.6 M-cycles step 120: timed with pme grid 96 96 96, coulomb cutoff 0.643: 7826.0 M-cycles step 180: timed with pme grid 104 104 104, coulomb cutoff 0.600: 6716.3 M-cycles step 240: timed with pme grid 100 100 100, coulomb cutoff 0.617: 7248.5 M-cycles optimal pme grid 104 104 104, coulomb cutoff 0.600 step 1900, remaining runtime: 7 s Writing final coordinates. step 2000, remaining runtime: 0 s NOTE: The GPU has 20% more load than the CPU. This imbalance causes performance loss, consider using a shorter cut-off and a finer PME grid. Core t (s) Wall t (s)(%)Time: 427.620 144.021 296.9 (ns/day)(hour/ns) Performance:2.401 9.996 By changing just the pme_order=6, I got this: Reading file test7.tpr, VERSION 4.6.1 (single precision) Using 1 MPI thread Using 4 OpenMP threads 1 GPU detected: #0: NVIDIA GeForce GT 630, compute cap.: 3.0, ECC: no, stat: compatible 1 GPU auto-selected for this run: #0 starting mdrun 'Protein in water' 2000 steps, 4.0 ps. step 60: timed with pme grid 104 104 104, coulomb cutoff 0.600: 6818.0 M-cycles step 120: timed with pme grid 96 96 96, coulomb cutoff 0.643: 7821.2 M-cycles step 180: timed with pme grid 104 104 104, coulomb cutoff 0.600: 6718.4 M-cycles step 240: timed with pme grid 100 100 100, coulomb cutoff 0.617: 7257.1 M-cycles optimal pme grid 104 104 104, coulomb cutoff 0.600 step 1900, remaining runtime: 7 s Writing final coordinates. step 2000, remaining runtime: 0 s Core t (s) Wall t (s)(%)Time: 550.020 144.580 380.4 (ns/day)(hour/ns) Performance: 2.392 10.035 I have run many test simulations by changing rlist, rcoulomb, rvdw, pme_order and fourierspacing
[gmx-users] disallowed residue calculation
Dear gmx users, Is there any gmx command to plot the number of residues in disallowed region of the Ramachandran plot. g_rama and xrama doesnot have such options to calculate the same. -Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 [EMAIL PROTECTED] --- - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: water molecules in vacuum simulation
Hi all, I am facing a problem in constraining the crystallographic water molecules during invacuo simulation. Even after including the oxygen atom numbers in the .top file for position restrain (given below), the dynamics is going the same way as it was without positoion restrain. Please Help me out of this. #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 12448 1 1000 1000 1000 12451 1 1000 1000 1000 12454 1 1000 1000 1000 12457 1 1000 1000 1000 12460 1 1000 1000 1000 12463 1 1000 1000 1000 12466 1 1000 1000 1000 12469 1 1000 1000 1000 12472 1 1000 1000 1000 12475 1 1000 1000 1000 12478 1 1000 1000 1000 12481 1 1000 1000 1000 12484 1 1000 1000 1000 12487 1 1000 1000 1000 12490 1 1000 1000 1000 12493 1 1000 1000 1000 12496 1 1000 1000 1000 12499 1 1000 1000 1000 12502 1 1000 1000 1000 12405 1 1000 1000 1000 #endif regards Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 [EMAIL PROTECTED] --- - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] defining 2 posres at a time in mdp
hi all, I want to define position restraints for a part of protein and water molecules also. I need to deinfe -DPOSRES and -DPOSRES_WATER at the same time. When I do it on separate lines in the mdp file, only first line is being read and accepted. Is there any way to include both of them in the same mdp file simultaneously. regards anwar - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: water molecules in vacuum simulation.
Hi all, I am performing in vacuum simulation of a protein containing crystallographic water molecules. I want to constrain these water molecules, but pdb2gmx program doesnot generate the pr.itp for water molecules. How do I constrain these water molecules. regards Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 [EMAIL PROTECTED] --- -REPLY TO- Date:Wed Sep 27 00:30:36 GMT+08:00 2006 FROM: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: gmx-users Digest, Vol 29, Issue 81 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: water molecules in vacuum simulation. (Steffen Wolf) 2. Re: surface tension (Serge Yefimov) 3. Re: EM problem with OPLS and TIP4P ([EMAIL PROTECTED]) 4. VAL group (Owen, Michael) 5. distance restraints: -merge (Owen, Michael) 6. Re: Which POPC Bilayer to start? (Jim Fonseca) -- Message: 1 Date: Tue, 26 Sep 2006 12:10:44 +0200 From: Steffen Wolf [EMAIL PROTECTED] Subject: Re: [gmx-users] water molecules in vacuum simulation. To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1 Hi Anwar, the answer is: Yes, sure. CU Steffen Dear users, Is it possible to perform an invacuum simulation with few constrained water molecules? I dont want to use the explicit solvent, but want to use the crystallographic water molecules in protein and perform invacuum simulation. regards Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 [EMAIL PROTECTED] --- - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Dipl.-Chem. Steffen Wolf Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: [EMAIL PROTECTED] Web: http://www.bph.rub.de -- Message: 2 Date: Tue, 26 Sep 2006 11:01:45 +0200 From: Serge Yefimov [EMAIL PROTECTED] Subject: Re: [gmx-users] surface tension To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Pri, Surface tension of 930.002 in gromacs units = 93.0002 mN/m or (dyn/cm) serge priyanka srivastava wrote: Dear all, what is the unit of surface tension in gromacs analysis? Is it dyn/cm or N/m. As according to me it is coming out to be in terms of N/m but it is attached with a conversion factor of some powers of 10. Kindly guide me. If I am getting e.g. 930.002 as the surface tension then what are it's units? regards, Pri... -- Message: 3 Date: Tue, 26 Sep 2006 09:22:46 -0400 From: [EMAIL PROTECTED] Subject: Re: [gmx-users] EM problem with OPLS and TIP4P To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=us-ascii -Original Message- From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Sent: Wed, 20 Sep 2006 10:28 PM Subject: [gmx-users] EM problem with OPLS and TIP4P Try this: unconstrained_start = no Also ensure that your .top file is correct. Also take a look at your starting positions, where is MW? Also ensure that your waters have the correct order: eg. 871SOL OW 3496 1.935 2.093 1.901 871SOL HW1 3497 1.902 2.172 1.945 871SOL HW2 3498 1.990 2.126 1.830 871SOL MW 3499 1.938 2.107 1.898 The problema was here. In my old tip4p.itp file the water sites were in reverse order. I just change the order and it works now. Thanks. Also try outputting coords for step 20,21,22,23 in the first system and see what is actually happening. ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx
[gmx-users] water molecules in vacuum simulation.
Dear users, Is it possible to perform an invacuum simulation with few constrained water molecules? I dont want to use the explicit solvent, but want to use the crystallographic water molecules in protein and perform invacuum simulation. regards Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 [EMAIL PROTECTED] --- - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] invacuo minimization
Dear gmx users, When I am minimizing a trimer protein in vacuum by SD as well as CG methods, one of the monomer gets apart from the rest of the protein and places itself away from the other two monomers, which are intact. No periodic box is assigned. But when I am running editconf and assigning a box, then the structures are intact. What is the reason for the above behaviour? I am pasting the em.mdp below: cpp = /lib/cpp define = -DFLEX_SPC constraints = none ;integrator = CG integrator = steep nsteps = 1000 ; ; Energy minimizing stuff ; emtol = 100 ;for SD emstep = 0.1 ;for CG ;emstep = 0.001 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 [EMAIL PROTECTED] --- - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: invacuo minimization
Hi David, I have checked the mdout.mdp and as you said it has pbc = xyz. What do I do now. I havent run editconf, but why it is taking pbc conditions? How do I remove these?? thanks Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 [EMAIL PROTECTED] --- -REPLY TO- Date:Thu Sep 07 18:00:08 GMT+08:00 2006 FROM: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: gmx-users Digest, Vol 29, Issue 14 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: invacuo minimization (David van der Spoel) 2. LIE energy calculation! (Mikko Hellgren) -- Message: 1 Date: Thu, 07 Sep 2006 10:44:52 +0200 From: David van der Spoel [EMAIL PROTECTED] Subject: Re: [gmx-users] invacuo minimization To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed [EMAIL PROTECTED] wrote: Dear gmx users, When I am minimizing a trimer protein in vacuum by SD as well as CG methods, one of the monomer gets apart from the rest of the protein and places itself away from the other two monomers, which are intact. No periodic box is assigned. But when I am running editconf and assigning a box, then the structures are intact. What is the reason for the above behaviour? I am pasting the em.mdp below: chekc your mdout.dmp, the default pbc = xyz cpp = /lib/cpp define = -DFLEX_SPC constraints = none ;integrator = CG integrator = steep nsteps = 1000 ; ; Energy minimizing stuff ; emtol = 100 ;for SD emstep = 0.1 ;for CG ;emstep = 0.001 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 [EMAIL PROTECTED] --- - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se -- Message: 2 Date: Thu, 07 Sep 2006 11:31:39 +0200 From: Mikko Hellgren [EMAIL PROTECTED] Subject: [gmx-users] LIE energy calculation! To: gmx-users@gromacs.org gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=us-ascii Hi Dear users, I have started to do calculations of the binding between a protein and different ligands. I have read articles on the LIE method and one tutorial. But still I have some quite general questions. I am using Cut-off and NVT ensamble. 1. When I run my ligands in a water solution without the protein, should I add counterions (Cl and Na) at physiological concentrations (about 10mM to 100mM) or make the system neutral with one or two ions or can I ignore any ions the simulation. 2. Should I put any restraints on the ligand in the simulation without the protein? 3. When I run my ligand bound to the protein. Should I put restraints (c-alpha, all atoms) on both protein and ligand or only protein or ligand or neither of them? My initial thought would be to put restraint on c-alpha of the protein and let the rest of the system be free. Mikko One cannot avoid making
[gmx-users] invacuo simulation
Dear gmx users, I am working on protein invacuo simulation in different condition like considering different box size (0.7, 0.8, 1.0) and also with and without pressure coupling. When I am looking at the rmsd and gyration results, they are all varying alot for all the simulations. The simulation seem to be equilibrated for a certain time and then but again they start deviating. I dont have any clue for why the system is showing a lot of discrepancies with in different simulations when they differ only in the box size. Can some on through some light on it? regards Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 [EMAIL PROTECTED] --- - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] theory of MD
Dear all, My question is on the theory of MD. I actually could not find any material which describes in detail about the time integration algorithm. 1) I wanted to know why the time integration algorithm has to be used, I mean the practical benefits of it. I want the reading reference for the same. 2) Also I have seen that there is no appropriate material which describes practically, i mean in detail from the Newtons laws of motion (taking few partiles as example and simulate it theoretically) and how the velocities, positions etc are claculated. I need the material for the same. Kindly give me the references for papers and tutorials. with best wishes Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 [EMAIL PROTECTED] --- - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] periodic boundary condition
Dear users, I want to apply the periodic boundary condition. So, the following options are sufficient or not? editconf_d -f xxx.gro -o xxx_box.gro -d 1.0 -c Or do we also have to give the option -pbc regards Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 [EMAIL PROTECTED] --- - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 28, Issue 63
hi maria, So, what parameters do I have to give in the mdp file for periodic boundary condictions, I thought just by applying the PBC through editconf will do the job. regards Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 [EMAIL PROTECTED] --- -REPLY TO- Date:Mon Aug 21 18:00:08 GMT+08:00 2006 FROM: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: gmx-users Digest, Vol 28, Issue 63 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: periodic boundary condition ( MGi? ) -- Message: 1 Date: Mon, 21 Aug 2006 10:13:27 +0200 From: MGi? [EMAIL PROTECTED] Subject: Re: [gmx-users] periodic boundary condition To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1 yes, they are sufficient. if I remember well, the flag -pbc does the opposite job, it removes periodic boundary conditions. anyway, remember to include in your mdp file the parameters for the treatment of periodic bonudary conditions! regards, Maria On 8/21/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Dear users, I want to apply the periodic boundary condition. So, the following options are sufficient or not? editconf_d -f xxx.gro -o xxx_box.gro -d 1.0 -c Or do we also have to give the option -pbc regards Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 [EMAIL PROTECTED] --- - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20060821/78f27cec/attachment-0001.html -- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users End of gmx-users Digest, Vol 28, Issue 63 * - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] invcuo and solvent simulation
Dear users, What are parameters which differs in invacuo and water simulation apart from that water is not added in invacuo. I mean what are the things we have to be considered or not considered while performing invacuo simulation. regards Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 [EMAIL PROTECTED] --- - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] comm_mode
Dear users, There is an option in .mdp named comm_mode, which deals with the transition and rotation of the molecule being simulated. I want to know why the transition and rotation happens during the simulation. Can any one suggest me any reading material where in I can find how the dynamics is performed internally. thanks in advance regards Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 [EMAIL PROTECTED] --- - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Vacuum simulation problem
Dear all, I am simulating a protein containing 2 domains which are linked together by a loop of around 10 residues. When I am simulating the same in vacuum, after approx 1ns, the rmsd has increased from 5 angstroms to 25 angstroms with in 10 time steps. You can surely imagine how drastic the structural changes are happening. What exactly might be happening there, why the protein is behaving like that. I am pasting the mdp file below. ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; title = Yo cpp = /lib/cpp constraints = all-bonds ;define = -DPOSRES integrator = md dt = 0.002; ps ! nsteps = 1000 ; total 1 ps. nstcomm = 1 nstxout = 500 nstvout = 500 nstfout = 500 nstlog = 500 nstenergy = 500 nstlist = 10 ns_type = grid rlist = 0.9 rcoulomb= 0.9 rvdw= 0.9 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = Protein ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 300 K. gen_vel = no gen_temp= 300.0 gen_seed= 173529 kindly guide me in this issue. regards Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 [EMAIL PROTECTED] --- - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] vacuum simulation problem
Dear all, I am simulating a protein containing 2 domains which are linked together by a loop of around 10 residues. When I am simulating the same in vacuum, after approx 1ns, the rmsd has increased from 5 angstroms to 25 angstroms with in 10 time steps. You can surely imagine how drastic the structural changes are happening. And also during the simulation after 500ps the protein started to rotate and later at approx 2ns the protein stopped rotation. What exactly might be happening there, why the protein is behaving like that. I am pasting the mdp file below. ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; title = Yo cpp = /lib/cpp constraints = all-bonds ;define = -DPOSRES integrator = md dt = 0.002; ps ! nsteps = 1000 ; total 1 ps. nstcomm = 1 nstxout = 500 nstvout = 500 nstfout = 500 nstlog = 500 nstenergy = 500 nstlist = 10 ns_type = grid rlist = 0.9 rcoulomb= 0.9 rvdw= 0.9 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = Protein ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 300 K. gen_vel = no gen_temp= 300.0 gen_seed= 173529 kindly guide me in this issue. regards Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 [EMAIL PROTECTED] --- - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: gmx-users Digest, Vol 28, Issue 28
-REPLY TO- Date:Wed Aug 09 18:00:10 GMT+08:00 2006 FROM: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: gmx-users Digest, Vol 28, Issue 28 Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://www.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to [EMAIL PROTECTED] You can reach the person managing the list at [EMAIL PROTECTED] When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: vacuum simulation problem (Gerrit Groenhof (RUG)) 2. Re: vacuum simulation problem (David van der Spoel) 3. Re: simulation at particular pH (Vojt?ch Spiwok) 4. Re: simulation at particular pH (Marc Baaden) -- Message: 1 Date: Wed, 09 Aug 2006 10:44:40 +0200 From: Gerrit Groenhof (RUG) [EMAIL PROTECTED] Subject: Re: [gmx-users] vacuum simulation problem To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi again, Yes, I have calculated the rmsd for individual domains and on of the individual domains not intact. So, it is clear that the rmsd is not due to the domain motion, but due to the structural changes with in the domain. This dynamics was run without any periodic boundaries. Later I have submitted another dynamics having defined a box (dictance 0.7 A) and comm_mode = Angular. 8ns of dynamics has been done and on analysis in vmd the structure is not rotating and the rmsd is alsostablizing after 1ns at around 5 A. There are no drasrtic structural changes seen. However, I think it is better if I run the dynamics without pressure coupling as you have suggested. Give me suggestions. regards Anwar In addition to Erik and my suggestions, you should also remove the overall rotation: comm_mode=linear. [EMAIL PROTECTED] wrote: Dear all, I am simulating a protein containing 2 domains which are linked together by a loop of around 10 residues. When I am simulating the same in vacuum, after approx 1ns, the rmsd has increased from 5 angstroms to 25 angstroms with in 10 time steps. You can surely imagine how drastic the structural changes are happening. And also during the simulation after 500ps the protein started to rotate and later at approx 2ns the protein stopped rotation. What exactly might be happening there, why the protein is behaving like that. I am pasting the mdp file below. ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; title = Yo cpp = /lib/cpp constraints = all-bonds ;define = -DPOSRES integrator = md dt = 0.002; ps ! nsteps = 1000 ; total 1 ps. nstcomm = 1 nstxout = 500 nstvout = 500 nstfout = 500 nstlog = 500 nstenergy = 500 nstlist = 10 ns_type = grid rlist = 0.9 rcoulomb= 0.9 rvdw= 0.9 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = Protein ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 300 K. gen_vel = no gen_temp= 300.0 gen_seed= 173529 kindly guide me in this issue. regards Anwar -- Mohd Anwaruddin Project Assistant C/o DR.H.A.Nagarajaram Lab of Computational Biology and Bioinformatics Center for DNA Fingerprinting and Diagnostics(CDFD) Nacharam Hyderabad-500 076 INDIA. Tel: +91-8413-235467,68,69,70 ext 2019 [EMAIL PROTECTED] --- - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Message: 2 Date: Wed, 09 Aug 2006 10:44:32 +0200 From: David van der Spoel [EMAIL PROTECTED] Subject: Re: [gmx-users] vacuum simulation problem To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed [EMAIL PROTECTED] wrote: Dear all, I am simulating a protein containing 2 domains which are linked together by a loop of around 10 residues. When I am simulating the same
[gmx-users] adding new residue (MSE) in topology database
hello, I am trying to add Selenomethionine (MSE) residue in to the topology database. And I have to calculate the van der waals parameters V(c6) and W(c12) as they have to be mentioned in ff???nb.itp, for which I have to get the sigma and epsilon values. Where can I find these valuse or how can I calculate them. thanks in advance Anwar - ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
