[gmx-users] Error in .top when running grompp for final product MD
Dear gromacs users, I am running MD for a protein with 212 amino acid residues. When I run grompp (grompp -f pn_md.mdp -c pn_md.pdb -r pn_md.pdb -p pn.top - o pn_md.tpr ) for the final product MD, I receive the following error message. I properly included sol and ion in the temperature control part of pn_md.mdp. If I include “define = -DPORRES” in pn_md.mdp, both grompp and mdrun work fine. The topolofy file pn.top worked well in the previous steps (em.mdp and pr.mdp). Any suggestions would be appreciated. Sanghwa Han [Error Message] creating statusfile for 1 node... ' for variable integrator, using 'md' Next time use one of: 'md' 'steep' 'cg' 'bd' 'sd' 'nm' 'l-bfgs' 'tpi' ' for variable ns-type, using 'Grid' Next time use one of: 'Grid' 'Simple' ' for variable coulombtype, using 'Cut-off' Next time use one of: 'Cut-off' 'Reaction-Field' 'Generalized-Reaction- Field' 'PME' 'Ewald' 'PPPM' 'Poisson' 'Switch' 'Shift' 'User' 'Generalized- Born' 'Reaction-Field-nec' 'Encad-shift' 'PME-User' ' for variable optimize_fft, using 'no' Next time use one of: 'no' 'yes' ' for variable tcoupl, using 'No' Next time use one of: 'No' 'Berendsen' 'Nose-Hoover' 'yes' 'Andersen' 'Andersen-interval' ' for variable Pcoupl, using 'No' Next time use one of: 'No' 'Berendsen' 'Parrinello-Rahman' 'Isotropic' ' for variable gen-vel, using 'no' Next time use one of: 'no' 'yes' ' for variable constraints, using 'none' Next time use one of: 'none' 'h-bonds' 'all-bonds' 'h-angles' 'all-angles' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4# checking input for internal consistency... ling /usr/bin/cpp : no such file or directory cpp: warning: '-x c' after last input file has no effect cpp: no input files cpp exit code: 256 -I/usr/local/gromacs/share/gromacs/top pn.top > gromppcHKNXc' ' command is defined in the .mdp file processing topology... processing coordinates... --- Program grompp, VERSION 3.3.1 Source code file: grompp.c, line: 448 Fatal error: number of coordinates in coordinate file (pn_md.pdb, 34158) does not match topology (pn.top, 0) --- ___ 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] Interaction energy calculation in a radius
Hi all, I want to calculate interaction energy between my ligand and residues of proetins which come within 6A of any atoms of the raidus. I have defined those residues and ligand as different groups. But how to select water around 6A radius of the ligand during dynamicsfor the calculation. If I consider all the water atoms for my calculation, huge contribution by water molecules, i guess is giving lots of background and so I am getting +ve values! Any suggestion would be highly appreciated alok ___ 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] dihedral
Dear Gromacs users, Thanks a lot for your input so far. my problem regarding the dihedral angle still suffering me. I need to rotate a bond by certain angle, say from 30 to 150 degrees. i would like to see how the peptide will change its conformation for example CIS to TRANS by the rotation. I tried to use as chris suggested below. but could not see any rotation around the bond. It is just fluctuating around its original bond but not rotating. can u help me. Thanks and regards Gajula >For example, my peptide is rotating 50 degrees about a bond B-C, out of >four bonded atoms A-B-C-D. I want to apply additional force on this > dihedral(B-C) during my simulation(only for this particular atoms to >make it rotate further till 180 degrees). All the remaining atoms in the >peptide will have normal force as usual. > May I ask you, how can I apply this in gromacs code. > Any help will be appreciated! The current manual is good at describing what the options do for dihedral restraints, but (to my knowlegde) doesn't explain at all how to get the implementation up and running. Here is how I have done it based on searching the mailing list for answers. I suggest that something like this is added by way of example to the manual for future releases. Also, the manual is a bit unclear about whether this type of dihedral restraint is stable for use near 180deg. I have found that for my system everything appears to behave normally and as expected over the entire range of dihedral angles including 180deg. In your .top file: ; Include forcefield parameters #include "ffoplsaa.itp" ; Include topologies #include "myprotein.itp" [ dihedral_restraints ] ; ai ajakal type label phi dphi kfac power AB C D 1 1 180 0 1 2 #include "tip4p.itp" etc... Make sure that the dihedral_restraints section comes immediately after the inclusion of the protein topology. If you have the protein topology directly in your .top file then just include dihedral_restraints after the protein listing but before any mention of things that are not that protein molecule. Add this to your .mdp ;dihedral restraints dihre = simple dihre_fc= 100 ; or whatever value you desire dihre_tau = 0.0 nstdihreout = 50 For more information about what these options mean, please refer to the manual. ___ 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
Re: [gmx-users] Are the constraint forces included intheforcesoutputed in the
Could you please tell me if the constraint forces are included in the forces outputed in the trr file? Constraint forces are not included. We should state this somewhere in the manual. I wondered about this before as well. Shouldn't we include them anyway? It is quite important when you use the forces for e.g. computing a You don't want to compute PMF from the forces in the trr file. You need a lot of sampling for a PMF and the trr would become far too big. Currently we have the pull code and free energy code, both with umbrella sampling and constraints for determining PMF's. I prefer to have F=-grad V in the trr file and not the constraint forces. Thank you very much for all your helps. That's great! The force without the constraint force is just what I want. For free energy calculation, I will use thermodynamics intergration or pull code. Thank you for your kind suggestion. I wondered about this before as well. Shouldn't we include them anyway? It might be a good idea to add an option to determine if writing the constraint force into trr file or not. How do you think? -- Pu _ Don't just search. Find. Check out the new MSN Search! http://search.msn.click-url.com/go/onm00200636ave/direct/01/ ___ 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] gromacs 4 release date?
Any projection date for a release? Of particular interest to me is whether it is very likely to come out before Jan 1 2008. I have heard that v4 is expected to scale better for parallel runs than previous versions, is this correct? If so, how close to the namd scaling might gromacs get? ___ 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
Re: [gmx-users] tau_p
> Hi, > > Well, tau_p rather controls how the pressure fluctuates around the > average..., ref_p is your attempt to control the average (if your > system is set up properly). Yeah, that :-) Mark ___ 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
Re: [gmx-users] problem with genion
No, i am not. you? On a serious note, bug 108 that David referred to (last modified this morning) suggests compilaton problems with gcc4 due to pbc.c, which doesnt sound healthy. The same bugzilla page has a possible cure with suggestion to use gcc3, but changing from one gcc to another is not something i like doing. I used icc 9.1 to compile gromacs-3.3.1. This solves the problem with genion I described earlier. All under suse 10.2. Incidentally, non-oss repositary of this distro includes gromacs-3.3.1. But that has also got a problem with genion. Send instant messages to your online friends http://uk.messenger.yahoo.com ___ 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
Re: [gmx-users] tau_p
Hi, Well, tau_p rather controls how the pressure fluctuates around the average..., ref_p is your attempt to control the average (if your system is set up properly). Cheers, Tsjerk On 1/5/07, Mark Abraham <[EMAIL PROTECTED]> wrote: > Dear all, > I am running md simulations on a decapeptide, using pressure coupling > [npt]. > My box is octahedral and box dimensions are set at peptide length plus > twice > the cut-off as recommended. I have set tau_p to be 1.0 ps. After 1 ns , > the > average pressure had come down to 2.6 bar, though fluctuations were quite > high. [Standard deviation 150.8 ] But after 6ns, the pressure has risen > again to 4.6 bar. Can you please advise me on this? What was your equilibration regime? Over what length of time are you calculating these average pressures? > Also, can you please > tell me if there is any correlation between pressure average and tau_p > values? Yes, there will be for a properly set-up system. Mark ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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
Re: [gmx-users] About g_cluster
Brigo et al. Biophys J. (2005) 88:3072 Smith et al. Proteins (2002) 48:487 Ciao Caterina Cesar Araujo ha scritto: Hi, Can anybody give some reference about a good explanation on how to use g_cluster in order to analyze a set of simulations on complexes differing one each other in their starting point conformation? Thanks in adavance, César.- --- Cesar Araujo, Lic. of Chemistry Research Center for Molecular Endocrinology P.O. Box 5000, FIN-90014 University of Oulu Finland phone: +358 8 3155632 e-mail: [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 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
Re: [gmx-users] problem with genion
> While using genion with -np 3, i get 2 lines of Replacing sol. xxx with Na > and it hangs up. With -np 1 it works fine and replaces 1 SOL with Na. I > thought it might be my system, so went to /tutor/speptide, but it was the > same behaviour. I am using gromacs 3.3.1. As I recall genion worked fine > under 3.2. That sounds very weird. Could you be running out of memory or some such? What was your full command line? Mark ___ 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
Re: [gmx-users] afm does not work!
> hi everyone > I need to pull the two parallel monolayers together,the two monolayers > are in the x-y plane , so i pull the one along the z direction,but it > stay still! i tried several times ,but all failed! > i use the > [position_restraints ] > 1 1 9 9 4000 > 2 1 9 9 4000 > the 1 and £²¡¡are the atoms in the long molecules that form the monolayers > ,if i decreased the fx,fy,fz,it show core fault and stopped! > the ; Force constants in kJ/(mol*nm^2) > afm_k1 = 10 > who can tell me why! I can't even understand your statement of your problem, never mind understanding the problem or helping to solve it. If you want people to give free help, please write clearly, in full sentences, describing what you wanted to do, what you actually did, what the error messages actually were, and do all of the above using sensible characters in sensible fonts. Mark ___ 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
Re: [gmx-users] tau_p
> Dear all, > I am running md simulations on a decapeptide, using pressure coupling > [npt]. > My box is octahedral and box dimensions are set at peptide length plus > twice > the cut-off as recommended. I have set tau_p to be 1.0 ps. After 1 ns , > the > average pressure had come down to 2.6 bar, though fluctuations were quite > high. [Standard deviation 150.8 ] But after 6ns, the pressure has risen > again to 4.6 bar. Can you please advise me on this? What was your equilibration regime? Over what length of time are you calculating these average pressures? > Also, can you please > tell me if there is any correlation between pressure average and tau_p > values? Yes, there will be for a properly set-up system. Mark ___ 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
Re: Re: Re: [gmx-users] Installation of Gromacs and speed...
> Thank you for the reply. I have some more queries: > So if I load Gromacs 3.3.1 on Octane will I gain on the time a bit ? Maybe... depends if there were any meaningful speed-ups in parts of the code you actually use. > Do you suggest me to update the Gromacs versions on both the systems to > Gromacs 3.3.1? Yes. > For this do I have to remove the older versions ? Will it over write. > Can I keep both the versions loaded on the system or will there be a > clash ? Save yourself some heartache and uninstall the old ones before installing the new ones. > Do I have to load fftw once again ? You can probably use the same fftw libraries, but you no longer need parallel ones for 3.3.1. Mark ___ 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
Re: [gmx-users] problem with genion
Abil Aliev wrote: While using genion with -np 3, i get 2 lines of Replacing sol. xxx with Na and it hangs up. With -np 1 it works fine and replaces 1 SOL with Na. I thought it might be my system, so went to /tutor/speptide, but it was the same behaviour. I am using gromacs 3.3.1. As I recall genion worked fine under 3.2. Send instant messages to your online friends http://uk.messenger.yahoo.com ___ 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 there is a problem compiling gromacs using gcc 4.x that may cause this. see a recent bugzilla entry about it. -- 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 ___ 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
Re: [gmx-users] problem regarding xmgr
sangeeta wrote: Dear GROMACS list members, It may be a very trivial question,But I can not solve it, please help,The commands like xmgrace,xpsview,xmgr, my-dssp are not working. How could I get out of that problem? regards Sangeeta -- Open WebMail Project (http://openwebmail.org) ___ 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 install the programs. -- 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 ___ 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] problem regarding xmgr
Dear GROMACS list members, It may be a very trivial question,But I can not solve it, please help,The commands like xmgrace,xpsview,xmgr, my-dssp are not working. How could I get out of that problem? regards Sangeeta -- Open WebMail Project (http://openwebmail.org) ___ 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] tau_p
Dear all, I am running md simulations on a decapeptide, using pressure coupling [npt]. My box is octahedral and box dimensions are set at peptide length plus twice the cut-off as recommended. I have set tau_p to be 1.0 ps. After 1 ns , the average pressure had come down to 2.6 bar, though fluctuations were quite high. [Standard deviation 150.8 ] But after 6ns, the pressure has risen again to 4.6 bar. Can you please advise me on this? Also, can you please tell me if there is any correlation between pressure average and tau_p values? I have attached the md parameters file and the mdout files with this mail. Thanks, Chetana. title = MDP file for Full MD cpp = /lib/cpp integrator = MD tinit = 0 dt = 0.002 nstcomm = 1 nsteps = 50 ; 1 ns (run control) nstxout = 1 nstvout = 1 nstxtcout = 250 nstenergy = 250 energygrps = Protein SOL ;(output control) nstlist = 10 ns_type = grid rlist = 1.1 ;(neighbor searching) coulombtype = PME ;rcoulomb_switch= 1.0 rcoulomb= 1.0 vdwtype = shift rvdw_switch = 0.9 rvdw= 1.0 fourierspacing = 0.12 ;(nm) ewald_rtol = 1e-5 pme_order = 4 ;(electrostatics and VDW) tcoupl = berendsen tc_grps = Protein SOL NA+ tau_t = 0.1 0.1 0.1 ref_t = 300 300 300;(Temperature coupling) ; pressure coupling is on pcoupl = berendsen tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = no constraints = all-bonds constraint_algorithm= lincs ; File 'mdout.mdp' was generated ; By user: chetana (501) ; On host: alanine ; At date: Mon Jan 1 12:28:06 2007 ; ; VARIOUS PREPROCESSING OPTIONS title= MDP file for Full MD cpp = /lib/cpp include = define = ; RUN CONTROL PARAMETERS integrator = MD ; Start time and timestep in ps tinit= 0 dt = 0.002 nsteps = 50 ; For exact run continuation or redoing part of a run init_step= 0 ; mode for center of mass motion removal comm-mode= Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Temperature, friction coefficient (amu/ps) and random seed bd-temp = 300 bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 10 emstep = 0.01 ; Max number of iterations in relax_shells niter= 20 ; Step size (1/ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1 nstvout = 1 nstfout = 0 ; Checkpointing helps you continue after crashes nstcheckpoint= 1000 ; Output frequency for energies to log file and energy file nstlog = 100 nstenergy= 250 ; Output frequency and precision for xtc file nstxtcout= 250 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = ; Selection of energy groups energygrps = Protein SOL ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist= 1.1 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.0 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon-r= 1 ; Method for doing Van der Waals vdwtype = shift ; cut-off lengths rvdw_switch = 0.9 rvdw = 1.0 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Spacing for the PME/
[gmx-users] problem with genion
While using genion with -np 3, i get 2 lines of Replacing sol. xxx with Na and it hangs up. With -np 1 it works fine and replaces 1 SOL with Na. I thought it might be my system, so went to /tutor/speptide, but it was the same behaviour. I am using gromacs 3.3.1. As I recall genion worked fine under 3.2. Send instant messages to your online friends http://uk.messenger.yahoo.com ___ 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] afm does not work!
hi everyone I need to pull the two parallel monolayers together,the two monolayers are in the x-y plane , so i pull the one along the z direction,but it stay still! i tried several times ,but all failed! i use the [position_restraints ] 1 1 9 9 4000 2 1 9 9 4000 the 1 and ２ are the atoms in the long molecules that form the monolayers ,if i decreased the fx,fy,fz,it show core fault and stopped! the ; Force constants in kJ/(mol*nm^2) afm_k1 = 10 who can tell me why! thanks ! ___ 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
Re: [gmx-users] Installation of Gromacs and speed...
Swamy Kakumani, Thank you for the reply. I am not working on the parallel machines, Linux version is Fedora Core 4 System's configuration is listed below in my previous mail. regards sharada -- Original Message -- From: swamy kakumani <[EMAIL PROTECTED]> To: [EMAIL PROTECTED] Date: Fri, 5 Jan 2007 08:26:29 + (GMT) Subject: [gmx-users] Installation of Gromacs and speed... sharada, it is better to load new version and uninstall the older version. you have to load new fftw. give the answers for following 1.are u working parallel or on one system? 2.mention your system configuration.? 3.ur linux version? swamy, bioinformatics centre, dept. of biochemistry, sri krishnadevaraya university, anantapur-515003 andhra pradesh sharada <[EMAIL PROTECTED]> wrote: Thank you for the reply. I have some more queries: So if I load Gromacs 3.3.1 on Octane will I gain on the time a bit ? Do you suggest me to update the Gromacs versions on both the systems to Gromacs 3.3.1? For this do I have to remove the older versions ? Will it over write. Can I keep both the versions loaded on the system or will there be a clash ? Do I have to load fftw once again ? Bothering you with too many questions ! Answers for these would help me to decide . Thanks in advance. sharada -- Original Message -- From: "Mark Abraham" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS users" Date: Thu, 4 Jan 2007 19:32:27 +1100 (EST) Subject: Re: Re: [gmx-users] Difference in the Forcefields and speed... > If I do the MD studies using Gromacs 3.1 and Gromacs 3.3 with differennt > forcefields like ffg43a1 and ffG53a5 respectively in the same simulating > conditions how different would be my results ? or will there be any > difference ? In theory both forcefield models are accurate representations of reality over the domain over which they were parametrized. There's no guarantee that they'd be similar to each other on a given domain, or to reality, and the further you get from their parameterization domain, the worse the chances. Ignoring a handful of bug fixes, gromacs 3.1 and 3.3 should produce similar ensembles, but they cannot be exactly the same. > Is there a difference in the speed of the simulations say if I run them > on SGI Octane R12000 and a Personal computer with 512 RAM Pentium III ? > Incidently Gromacs 3.1 is loaded on Octane and Gromacs 3.3 on Pentium III Yep. > Why I am asking the second question is that the time taken on Octane is > much larger ( around 9 days) compared to the Pentium III (3 days) what may > be the reason ? Probably, the assembly-language optimized inner loops are being used on the PIII, and generic inner loops on the Octane. The vast majority of MD simulation time is spent in these loops, so they are critical to performance. Obviously, native CPU speed is also an issue here too. Mark ___ gmx-users mailing list gmx-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 mailing list gmx-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 Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php ___ 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
Re: [gmx-users] Are the constraint forces included inthe forcesoutputed in the
From: David van der Spoel <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: Re: [gmx-users] Are the constraint forces included inthe forcesoutputed in the Date: Fri, 05 Jan 2007 10:40:18 +0100 Berk Hess wrote: From: "Pu Liu" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: [gmx-users] Are the constraint forces included in the forcesoutputed in the trr file? Date: Fri, 05 Jan 2007 00:34:03 + Dear GROMACS list members, Could you please tell me if the constraint forces are included in the forces outputed in the trr file, or just used to propagate the system? Constraint forces are not included. We should state this somewhere in the manual. Berk. I wondered about this before as well. Shouldn't we include them anyway? It is quite important when you use the forces for e.g. computing a You don't want to compute PMF from the forces in the trr file. You need a lot of sampling for a PMF and the trr would become far to big. Currently we have the pull code and free energy code, both with umbrella sampling and constraints for determining PMF's. I prefer to have F=-grad V in the trr file and not the constraint forces. Berk. _ Play online games with your friends with Messenger http://www.join.msn.com/messenger/overview ___ 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
Re: [gmx-users] Are the constraint forces included in the forcesoutputed in the
Berk Hess wrote: From: "Pu Liu" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: [gmx-users] Are the constraint forces included in the forcesoutputed in the trr file? Date: Fri, 05 Jan 2007 00:34:03 + Dear GROMACS list members, Could you please tell me if the constraint forces are included in the forces outputed in the trr file, or just used to propagate the system? Constraint forces are not included. We should state this somewhere in the manual. Berk. I wondered about this before as well. Shouldn't we include them anyway? It is quite important when you use the forces for e.g. computing a PMF. -- 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 ___ 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
RE: [gmx-users] Are the constraint forces included in the forcesoutputed in the
From: "Pu Liu" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: [gmx-users] Are the constraint forces included in the forcesoutputed in the trr file? Date: Fri, 05 Jan 2007 00:34:03 + Dear GROMACS list members, Could you please tell me if the constraint forces are included in the forces outputed in the trr file, or just used to propagate the system? Constraint forces are not included. We should state this somewhere in the manual. Berk. _ Live Search, for accurate results! http://www.live.nl ___ 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
