Re: [gmx-users] the code speed between Gromacs 3.0 and Gromacs 4.0

Dechang Li wrote: Dear gmx-users, Are there any comparisons of the code speed between Gromacs 3.0 and Gromacs 4.0. In my calculation, I got a speed about 3.5ns/day of a system have about 50,000 atoms, using 8 CPUs with Gromacs 3.3.1. In contrast, the speed can reach up to 7.3ns/day when switch

[gmx-users] the code speed between Gromacs 3.0 and Gromacs 4.0

Dear gmx-users, Are there any comparisons of the code speed between Gromacs 3.0 and Gromacs 4.0. In my calculation, I got a speed about 3.5ns/day of a system have about 50,000 atoms, using 8 CPUs with Gromacs 3.3.1. In contrast, the speed can reach up to 7.3ns/day when switch to Gromac

[gmx-users] trjconv -pbc: how to keep all parts of the system "clustered" together in PDB?

Search: trjconv pbc cluster on the gromacs mailing list and take a look at the first hit. Basically, you need to find a frame that *does* work with -pbc cluster and then make a new .tpr based on the clustered .gro and then run trjconv -pbc mol. Just ensure that this frame is as close to the

Re: [gmx-users] Problems with umbrella sampling

Amir Marcovitz wrote: Hi, my system is constructed of 2 parallel plates in a box with solvent. each plate is made of 36 atoms which are positively charged on one of them (SRP) and negatively charged on the other plate (SRN). i want to perform a simulation with umbrella sampling between th

[gmx-users] Problems with umbrella sampling

Hi, my system is constructed of 2 parallel plates in a box with solvent. each plate is made of 36 atoms which are positively charged on one of them (SRP) and negatively charged on the other plate (SRN). i want to perform a simulation with umbrella sampling between the 2 so i defined the pulling s

Re: [gmx-users] trjconv -pbc: how to keep all parts of the system "clustered" together in PDB?

I thought I was sure -pbc cluster will work, but it doesn't :( trjconv get's stuck on an infinite loop while calculating center of mass. In an index.ndx I created a new group which I called CLUSTER, as Mark suggested (I used make_ndx), then I ran trjconv: trjconv -f 1Y2Elig_em.trr -s 1Y2Elig_em

[gmx-users] conversion between harmonic bonds/angles and GROMOS96 bonds/angles

I am interested in converting between GROMOS96 bond/angle potentials and standard harmonic potentials. The GROMACS manual (version 4) suggests formulae for doing so (Eq. 4.38 and Eq. 4.53). However, I am having trouble understanding where these come from and find that they seem to give rather po

Re: [gmx-users] Replica Exchange MD on more than 64 processors

bharat v. adkar wrote: On Mon, 28 Dec 2009, David van der Spoel wrote: bharat v. adkar wrote: On Mon, 28 Dec 2009, Mark Abraham wrote: > bharat v. adkar wrote: > > On Sun, 27 Dec 2009, Mark Abraham wrote: > > > > > bharat v. adkar wrote: > > > >On Sun, 27 Dec 2009, Mark Abraham wrot

Re: [gmx-users] protein simulation

edmund lee wrote: Dear all, I am trying to do a simulation of protein OMPA. At the step grompp, it shows a fatal error stated " Fatal error: Atomtype 'HC' not found!" I tried to configure the error but i failed. So, hope that anyone can help me in this. There are various underlying causes.

Re: [gmx-users] convert B-factor

Hi Antonio, You can do something like: grep -v "^#@" rmsf1.xvg > rmsf1.dat grep -v "^#@" rmsf2.xvg > rmsf2.dat paste rmsf1.dat rmsf2.dat | awk '{print $4-$2}' > difference.dat That will give you a file with the rmsf difference. You can use editconf to read such data into the b-factor field, alth

Re: [gmx-users] Replica Exchange MD on more than 64 processors

On Mon, 28 Dec 2009, David van der Spoel wrote: bharat v. adkar wrote: On Mon, 28 Dec 2009, Mark Abraham wrote: > bharat v. adkar wrote: > > On Sun, 27 Dec 2009, Mark Abraham wrote: > > > > > bharat v. adkar wrote: > > > >On Sun, 27 Dec 2009, Mark Abraham wrote: > > > > > > >bh