[gmx-users] molecule broken

Dear All, I am running a simulation for a RNA system using 50 cpus with gromacs 3.3.1. At some frames, my molecule is broken, that is parts of the molecule are on opposite sides of the periodic box. This problem was reported sometime ago (Nov. 2006) and David suggested to submit the bugzilla.

Re: [gmx-users] NMA for a group

Hi Christian, Perhaps, I made a mistake in describing my problem. I can not believe, that no one ever tried this before. I have a phosphate in water and want to calculate the hessian just for the phosphate. How do I do that? I have done something similar like what you want to do. I calculate t

Re: [gmx-users] rotational fit in XY plane only

Currently there is not. I would like to have that feature as well. can't you simply set all z-coordinates to zero and carry out a 3D fit as usual? (you may get a problem with mirror images, but the handedness is anyway not anymore uniquely defined once you project on 2D). I don't think so. I

Re: [gmx-users] compare simulations between wt and mutate protein

Hi, Hi Andrea, I think it's a good thing to start another simulation by mutating the [EMAIL PROTECTED] Besides, it would be good to mutate the [EMAIL PROTECTED] back, to see if it goes the other way. In any case, you'll have to perform multiple simulations. For a strategy on comparing simulat

[gmx-users] radial distribution function

Hi All, I would like to compute the radial distribution function g(r) between solvent molecules and a group of atoms of the solute. To this end, I define two groups in the index.ndx file: one for solvent and one for a peptide group. The index file looks like: [ Pep ] 1 2 3 4 [ Sol] 10 11 12 ...

Re: [gmx-users] Arbitrary S-S bonds

Hi, Can anybody tell me how can I generate arbitrary S-S bonds with gromacs? The problem is that I have a protein and I want to specify some S-S bond between two cysteine residues but they are not an options given by pdb2gmx -ss. Should I touch topology file by hand? Why pdb2gmx do not recog

Re: [gmx-users] Is 2D projection

Dear gmx users, Does the 2D projection plot has something to do with convergence of the trajectory? If so, what kind of shape of plot shows the trajectory is non-converged? Normally, I use RMSD plot to see if the trajectory tends to converge. Now my concern is how to see whether trajectory is

[gmx-users] problem with g_sas

Dear All, I have been using two versions of gromacs to calculate the solvent accessible surface for one peptide. However, I got totally different results: with g_sas (3.1.4) - @ s0 legend "Hydrophobic" @ s1 legend "Hydrophilic" @ s2 legend "Total" @ s3 legend "D Gsolv" 0

Re: [gmx-users] second derivative of force

Hi, thanks Mark for the suggestion. I made an mistake in writing the first email. Actually, I need the first derivative of force, i.e, the second derivative of total energy. Perhaps, a modification the code that computes the Hessian is a good idea. To do this, does anyone know exactly where

[gmx-users] second derivative of force

Dear All, I would like to obtain the second derivative of the total force d^2f_i/dr_i^2 at every atom i along the trajectory. In principle, this can be obtained from the Hessian matrix. However, I don't need the cross terms like d^2f_i/dr_i dr_j, therefore it will be very time consumming to ca

Re: [gmx-users] hi

> hi today i have tried to run the position restrained dynamics using my tpr > file > grompp -f pr.mdp -c 7/trp_b4pr.gro -p 1/trp.top -o 8/trp_pr.tpr > > But its showing the error > Fatal error: > number of coordinates in coordinate file (7/trp_b4pr.gro, 14580) > does not match topo

Re: [gmx-users] how to do simulation at high temperature

> That is the same as reducing the timestep! not really. If one runs simulations at high temperature with the original mass then the kinetic energy becomes very high--> simulations maybe crashed. By increasing mass then the kinetic energy is reduced and the simulations are more stable. Check: Pro

Re: [gmx-users] how to do simulation at high temperature

Hi, you should increas the mass of atoms. Phuong > I want to simulate a short peptide in solution at high temperature (e.g. > T=800). Because of the large momentum of molecules, it is very easy to > have bad contacts to cause the system to crash. One way to prevent it is > to reduce the time s

Re: [gmx-users] N-terminus type PRO-NH

> > Is pdb2gmx recognising the N-terminal residue as PRO? > I think so. However in my case pdb2gmx does not read the entry PRO-NH in the ffG43a1-n.tdb file. Only NH3+,NH2, or None are read. I cheat pdb2gmx by replacing the header [ PRO-NH ] by [ NH2 ] and it works for me now. Phuong

[gmx-users] N-terminus type PRO-NH

Dear All, I would like to have the N-terminus type PRO-NH for my molecule. I saw this option is available in the ffG43a1-n.tdb file but pdb2gmx does not provide this option (only NH3+,NH2, or None are available). Does anyone know how to get this N-terminus type? Many thanks for any help. Phuo