Re: [gmx-users] Gromacs setup on dual core machine

Hello! I have a similar problem with installing gromacs on a dual core machine. When I go through the procedure described by Matheus Fazian Ige Gondo a bit further down installing lam/mpi then fftw and finally gromacs everything seems to be working fine, but lam/mpi doesn't recognize the two co

Re: [gmx-users] Gromacs setup on dual core machine

Jens Pohl wrote: Hello! I have a similar problem with installing gromacs on a dual core machine. When I go through the procedure described by Matheus Fazian Ige Gondo a bit further down installing lam/mpi then fftw and finally gromacs everything seems to be working fine, but lam/mpi doesn't rec

Re: [gmx-users] Gromacs setup on dual core machine

Jens Pohl wrote: Hello! I have a similar problem with installing gromacs on a dual core machine. When I go through the procedure described by Matheus Fazian Ige Gondo a bit further down installing lam/mpi then fftw and finally gromacs everything seems to be working fine, but lam/mpi doesn't rec

Re: [gmx-users] Gromacs setup on dual core machine

> > Jens Pohl wrote: > > Hello! > > > > I have a similar problem with installing gromacs on a dual core machine. > > When I go through the procedure described by Matheus Fazian Ige Gondo a bit > > further down installing lam/mpi then fftw and finally gromacs everything > > seems to be working

[gmx-users] results of energy minimization

Dear gromacs experts, I have run the energy minimization of a protein.With the tail command it shows the following results: [EMAIL PROTECTED]:~/protein> tail -15 md.log NS-Pairs 94.365846 1981.68276620.0 Reset In Box 0.5693855.124465

Re: [gmx-users] results of energy minimization

Hello! Check out http://wiki.gromacs.org/index.php/Errors#Stepsize_too_small.2C_or_no_change_in_energy._Converged_to_machine_precision.2C_but_not_to_the_requested_precision Cheers /Per 12 mar 2008 kl. 11.58 skrev s lal badshah: Dear gromacs experts, I have run the energy minimization of a pr

[gmx-users] How to judge the system was equilibrated

Dear all! I ran a simulation of a ligand bound to an enzyme,and I want know when the system achieved equilibration. Can I judge it from rmsd or potential? Which rmsd should I obtained? the backbone protein or the drug ligand? Thanks in advance! ___ g

Re: [gmx-users] results of energy minimization

Quoting s lal badshah <[EMAIL PROTECTED]>: > Dear gromacs experts, > I have run the energy minimization of a protein.With the tail command it > shows the following results: > [EMAIL PROTECTED]:~/protein> tail -15 md.log > NS-Pairs 94.365846 1981.68276620.0 > Reset

[gmx-users] DMSO G53a6 FF in Gromacs

Dear Gromacs Users, I simulated the preequilibrated box of DMSO that is located in the Gromacs Force Field Distribution with the G53a6 Gromos FF parameters (adapted from the Geerke et. al paper in J Phys Chem B, 108 (2004)). After temperature equilibration I performed a NPT run but in contrast

Re[3]: [gmx-users] size of the system

> The correct file to use is spc216.gro (which genbox automatically finds in > the GROMACS $GMXLIB/top directory). I'm guessing that genbox is finding a > local spc216.pdb which is somehow broken. Thanks a lot. I've fixed the problem translating ".pdb" to ".gro" It was really something wrong with .

[gmx-users] Re: DMSO G53a6 FF in Gromacs

Hi Berk, Thanks for replying so quick. I made it rigid in that way that I used bonded interactions also for the groups that are not directly connected (FF parameters gb_49 & gb_50) and then applied all-bond SHAKE. For the other bonds I used gb_41, gb42 and for the three angles ga_45 and ga_46.

RE: [gmx-users] DMSO G53a6 FF in Gromacs

Hi, Did you make your DMSO molecule completely rigid? Berk. > Date: Wed, 12 Mar 2008 12:18:08 +0100 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: [gmx-users] DMSO G53a6 FF in Gromacs > > Dear Gromacs Users, > > I simulated the preequilibrated box of DMSO that is located in t

Re: [gmx-users] DMSO G53a6 FF in Gromacs

On Wed, 12 Mar 2008 12:24:02 +0100 Berk Hess <[EMAIL PROTECTED]> wrote: Hi, Did you make your DMSO molecule completely rigid? Should we really worry about such a difference in density? (1095-1108)/1095=0.012 How precise is the value reported? Did you estimate the error by using different sec

Re: [gmx-users] DMSO G53a6 FF in Gromacs

First thanks for the answers. I checked several sections of the trajectory, but the deviation is always the same, even when disregarding the first 500 ps or looking only at the last 500 ps of the trajectory where everything is nice equilibrated. I think the error is insignificantly small (howev

Re: [gmx-users] Re: DMSO G53a6 FF in Gromacs

Hi Berk, I used weak berendsen temperature coupling with tau_t = 0.1 and a ref_t of 298.15 K. My average temperature during the NPT run (disregarding the first 100 ps) is ca. 298.20 K (as given by g_energy). I had another question to you, Berk, in my last mail to the list maybe two hours ago,

RE: [gmx-users] Re: DMSO G53a6 FF in Gromacs

> Date: Wed, 12 Mar 2008 12:31:12 +0100 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: [gmx-users] Re: DMSO G53a6 FF in Gromacs > > Hi Berk, > > Thanks for replying so quick. I made it rigid in that way that I used > bonded interactions also for the groups that are not dire

[gmx-users] orires energy terms

Hi, "Orient.-Rest." is the potential energy of the restraints (in kJ/mol). "Ori.-R.-RMSD" is the RMS deviation of the orientations in units of your orientation observable input. Berk. > > There is another question that could possibly be answered by Berk: I > often use his Orientation Restrain

[gmx-users] RE: Coul-14, LJ-14 and RF-excl definitions (2)

Dear developers, I would again like to thank David, Xavier and Berk for their very informative explanations on RF-excl and 1-4 interactions. I am still a bit confused, though, with Berk's very last statement on this issue. If I quote it: "The reaction field is not applied to pair (1-4) terms. The

RE: [gmx-users] RE: Coul-14, LJ-14 and RF-excl definitions (2)

Hi, The RF correction is NOT applied to 1-4 pairs. It is applied to excluded pairs, independently of it they interact via 1-4 interaction or not. For RF simply all atom pairs in a cut-off sphere need to be corrected. The simplest way of doing this is correcting the non-bonded potential and correc

Re: [gmx-users] Re: DMSO G53a6 FF in Gromacs

Dear all, I think I found the reason for the deviation after "hunderds of small runs"...:-): I normally used Dispersion Correction for both the energy and pressure because in the manual the following is noted: "...The pressure correction in contrast is very large and can not be neglected. Al

RE: [gmx-users] Re: DMSO G53a6 FF in Gromacs

> Date: Wed, 12 Mar 2008 17:20:19 +0100 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Re: DMSO G53a6 FF in Gromacs > > Dear all, > > I think I found the reason for the deviation after "hunderds of small > runs"...:-): I normally used Dispersion Correction f

Re: [gmx-users] problem with mpi configuration.

Thank you very much for help me. I have try to install gromacs 3.3.3 on rhel 4.0. I try to configure gromacs single with the command "./configure --enable-mpi --program-suffix=_mpi--prefix=/usr/local/gromacs332", but when I try to install, I have this error: usr/bin/install: cannot creat

[gmx-users] trjconv output at a specified time

Hi, I want to output a structure in a given time, for example , in step 1 during minimization. I tried the following command using dump: trjconv -f r-l_1_oplsaa.minim_traj.trr -timestep 1 -o m.pdb -s r-l_1_oplsaa.input.tpr -t0 0 -dump 1 But It didnot work. Output msg: Select a group: 2 Selec

Re: [gmx-users] trjconv output at a specified time

You asked for the frame at 1ps. The trajectory starts at 125ps, so unsurprisingly the program does not give you an output. - Original Message From: Liu Shiyong <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Wednesday, March 12, 2008 10:07:17 PM Subject: [gmx-users] tr

Re: [gmx-users] trjconv output at a specified time

Thanks. The trajectory starts at 125ps ? So step 1 == 125 ps step 2 == 250 ps step 3 == 375 ps Where is 125ps from ? But ; RUN CONTROL PARAMETERS integrator = steep ; Start time and timestep in ps tinit= 0 dt = 0.002

Re: [gmx-users] problem with mpi configuration.

/usr/local/gromacs/bin/grompp_mpi_d--prefix=/usr/local/gromacs333 <<= just zoom in the middle of the command right here: mpi_d--prefix= you forgot to put a space between "mpi_d" and "--prefix" copy&paste the corrected version bellow. ./configure --enable-mpi --program-suffix=_mpi --prefix=/usr

Re: [gmx-users] trjconv output at a specified time

Select a group: 2 Selected 2: 'Protein-H' trn version: GMX_trn_file (single precision) Reading frame 0 time 125.000 'nuff said. Couldn't comment on the time between frames in your file. gmxdump will tell you, or get it from (nstxout or nstxtcout)*dt in your mdp. - Original Message