[gmx-users] Comparing amplitudes of motions in two MD simulations

Hello, I would like to compare amplitude of motion of a specific atom in two sets of MD simulations. Something like rms of displacements about the equilibrium position would do. In your experience, which gromacs analysis tools would be suitable for this? Any other insight into how this can be done

[gmx-users] xtc-precision

>* You need to choose a large .xtc precision, or use nstxout and filter the >group*>* afterwards.* * * *I tried xtc-precision=100. This gives the same result as the default value **xtc-precision=1000. Yet, the results are different from the analysis of the trr file.* -- gmx-users mailing li

[gmx-users] xtc-precision

I would like to save disk space and write only protein coordinates using xtc-grps, but preserve the same precision as in trr file. What value of xtc-precision should be used to achieve this? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Plea

Re: [gmx-users] to gro or not to gro

On Sun, Nov 27, 2011 at 11:26 AM, Mark Abraham wrote: > On 27/11/2011 10:15 PM, Igor Druz wrote: > > write to gro in angstroms, read from gro in angstroms, convert into nm in > grompp. > > > What are you trying to communicate with this hypothetical workflow? > > Hi

Re: [gmx-users] to gro or not to gro

Changing the format > to %9.4f will break everything written in fortran. And, yes, people > still use fortran. So which point did I miss? :) > > Cheers, > > Tsjerk > > > On Sun, Nov 27, 2011 at 11:38 AM, Igor Druz wrote: > > You are missing the point. Quoting my respon

Re: [gmx-users] to gro or not to gro

ot us against you, and I'm sorry > you have to go through this. Trust me, most of us have had such > moments, although with a different aspect. > > Best, > > Tsjerk > > On Sun, Nov 27, 2011 at 11:03 AM, Igor Druz wrote: > > You can put whichever spin you like into what

Re: [gmx-users] to gro or not to gro

You can put whichever spin you like into what is said, but there is a clear (and unnecessary) fault with the way coordinates are stored in gro files when made from pdb using pdb2gmx. On Sun, Nov 27, 2011 at 12:39 AM, Mark Abraham wrote: > On 27/11/2011 5:07 AM, Igor Druz wrote: > > On

Re: [gmx-users] to gro or not to gro

On Sat, Nov 26, 2011 at 6:37 PM, David van der Spoel wrote: > On 2011-11-26 19:07, Igor Druz wrote: > >> On Sat, Nov 26, 2011 at 5:35 PM, > <mailto:chris.neale@utoronto.**ca >> wrote >> >> >>1. why repeat the calculations? If you're talking a

Re: [gmx-users] to gro or not to gro

On Sat, Nov 26, 2011 at 5:35 PM, wrote > 1. why repeat the calculations? If you're talking about simulations then > there is no need to repeat them due to this. You will get different answers > with the same starting coordinates if you simply change the initial > velocities. If you're talking abo

Re: [gmx-users] to gro or not to gro

I already knew the reason. But I had to find this out hard way. Now facing a dreading prospect of repeating tons of calculations! Hence the request for the "bad for the health" sign. Btw, gromacs issues a lot of warnings, but not this one :D What a bright idea to switch from angstroms to nanomete

[gmx-users] to gro or not to gro

There was no water. Version 4.5.5. Single precision. This is what I ran: pdb2gmx -f 1.pdb -p g1 -o g1 grompp -f 1.mdp -c g1.gro -o g1.tpr -p g1.top mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene Potential energy: 1.19780e+02 kJ/mol grompp -f 1.mdp -c 1.pdb -o g1.tpr -p g1.top mdrun -v -s g1.tp

[gmx-users] to gro or not to gro

There is something not quite right here. I grompp a gro file created from a pdb file using pdb2gmx and run MD to do a single point energy calculation. I then grompp the original pdb file and run MD to do a single point energy calculation. The values of potential energy values are different by ab

[gmx-users] vol in mdrun output

"vol 0.63! imb F 25% pme/F 0.99 step 16389600..." What does vol 0.63! stand for ? -- 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 p

[gmx-users] NPT or NVT for calculating averaged experimental parameters

Hi there, Is there any consensus on whether to use NVT or NPT runs for calculating averaged NMR parameters in water at room temperature? I have seen some papers which use NPT, others use NVT. Thanks you, Igor -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/lis

Re: [gmx-users] Reproducable MD runs on two PCs

compilation? Igor On Sun, Nov 20, 2011 at 9:16 AM, Mark Abraham wrote: > On 20/11/2011 7:31 PM, Igor Druz wrote: > > I recompiled gromacs, lam, fftw3 on both PCs with the same version of > intel compilers (before they were different, v. 10 & 12), set gen_vel=no > and optimize_fft

Re: [gmx-users] Reproducable MD runs on two PCs

1 10:10 PM, Igor Druz wrote: > > Hello, > > I am running MDs on a linux PC with OpenSuse, using: > > mpirun -np 4 mdrun -v -dlb auto -reprod > > If I repeat the calculation on the same PC, I get the same result. If I > change to another PC with RedHat I get a

[gmx-users] Speeding up g_angle calculations

Hello, Is there any way to speed up g_angle calculations ? Thank you, Igor -- 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 (u

[gmx-users] Reproducable MD runs on two PCs

Hello, I am running MDs on a linux PC with OpenSuse, using: mpirun -np 4 mdrun -v -dlb auto -reprod If I repeat the calculation on the same PC, I get the same result. If I change to another PC with RedHat I get a different result. More specifically, I am calculating a deviation from experim