Re: [gmx-users] S-type Hydrogen bond correlation function

Ramachandran G wrote: Yes, i do write velocities to output trajectory at 10 fs. But i understood from the thread(below link) that 'trjorder' do not save the velocities http://oldwww.gromacs.org/pipermail/gmx-users/2003-May/005681.html I don't know is there any other way we can do it in the

[gmx-users] How to get centre of mass bond & angle distribution

Hi,   I am trying to coarse-grain a system. For that I want to optimize the bond , angle and dihedral parameters of coarse-grained model based on atomistic simulation. For that, in the atomistic simulation part, I want to calculate the the distribution of 'effective' angle made by the 'centre of

Re: [gmx-users] S-type Hydrogen bond correlation function

Yes, i do write velocities to output trajectory at 10 fs. But i understood from the thread(below link) that 'trjorder' do not save the velocities http://oldwww.gromacs.org/pipermail/gmx-users/2003-May/005681.html I don't know is there any other way we can do it in the new version. Thanks. Ra

Re: [gmx-users] S-type Hydrogen bond correlation function

Ramachandran G wrote: Thank you, I have installed new version of gromacs4.0.5 and trjorder works fine in giving me the trajectory file(ordered.trr) but using this file when i try g_velacc(velocity autocorrelation function) for the water molecules, i am getting the result 'nan 0.000'. Later w

Re: [gmx-users] S-type Hydrogen bond correlation function

Thank you, I have installed new version of gromacs4.0.5 and trjorder works fine in giving me the trajectory file(ordered.trr) but using this file when i try g_velacc(velocity autocorrelation function) for the water molecules, i am getting the result 'nan 0.000'. Later when i checked the trajec

Re: [gmx-users] Modify disre_fc during md

Andrei Istrate wrote: Andrei Istrate wrote: I would like to modify the force constant of some distance constraints during my MD. I know this is not implemented in GROMACS and I'd like to modify the code. I have read that it could be done in md.c, but I didn't find the variable dr_fc in this fi

Re: [gmx-users] EM with inflategro

sunny mishra wrote: I did the catting of lipid.gro and protein.gro and named it as system.gro and then I inflated DSPC using INFLATEGRO script command and also I am using the default value of 14A for cut off distance. So I don't have much idea that after inflating the whole system if I run th

Re: [gmx-users] EM with inflategro

I did the catting of lipid.gro and protein.gro and named it as system.gro and then I inflated DSPC using INFLATEGRO script command and also I am using the default value of 14A for cut off distance. So I don't have much idea that after inflating the whole system if I run the EM then protein and lipi

Re: [gmx-users] EM with inflategro

sunny mishra wrote: Hi All, I am having a trouble during EM step after I inflategro my lipid.gro (protein is already centered). After doing this : Reading.

[gmx-users] EM with inflategro

Hi All, I am having a trouble during EM step after I inflategro my lipid.gro (protein is already centered). After doing this : Reading. Scaling lipids There are 512 lipids... with 14 atoms per lipid.. Determining upper and lower leaflet... 240 lipids in the upper... 272 lipids in th

Re: [gmx-users] trjcat xtc files

Paymon Pirzadeh wrote: Hi Tom, Thanks for the tip. It worked on the command line and I had 3000 frames. But when I fed the file to VMD, it showed only 1800 frames!? Although the initial and final configurations looked correct. I still am not sure what possibly goes wrong!? VMD is not an appr

[gmx-users] Modify disre_fc during md

>Andrei Istrate wrote: >> >> I would like to modify the force constant of some distance constraints >> during my MD. >>I know this is not implemented in GROMACS and I'd like to modify the code. >> I have read that it could be done in md.c, but I didn't find the variable >> dr_fc in this file. >W

Re: [gmx-users] trjcat xtc files

Apparently you are right! But my desktop has 4GB RAM, and to be honest, when I load normal trajectories (I know they are smaller in size) but I have not seen such issue in almost 60% increase in RAM occupation by VMD. Normally I load 1000 frames, and now I want 3000 frames. Why should it run to suc

Re: [gmx-users] trjcat xtc files

On Nov 2, 2009, at 18:13, Paymon Pirzadeh wrote: Hi Tom, Thanks for the tip. It worked on the command line and I had 3000 frames. But when I fed the file to VMD, it showed only 1800 frames!? Although the initial and final configurations looked correct. I still am not sure what possibly

RE: [gmx-users] trjcat xtc files

Hi Tom, Thanks for the tip. It worked on the command line and I had 3000 frames. But when I fed the file to VMD, it showed only 1800 frames!? Although the initial and final configurations looked correct. I still am not sure what possibly goes wrong!? Payman On Mon, 2009-11-02 at 10:50 +, TJ

[gmx-users] normal mode analysis

Hi Gromacs User's, In the normal mode analysis if I get the first 6 eigenfrequency zero then I can think that the the protein is properly energy minimized. Thank you Abhijit ___ gmx-users mai

Re: [gmx-users] Quick question about g_mindist

Hi Justin, thanks for your answer Justin A. Lemkul ha scritto: >> I am using g_mindist to see how close get C-alphas to each other in my >> chains. What I do is selecting C-alpha two times when prompted. I have >> only a quick question, just to be sure: The script doesn't take into >> account the

[gmx-users] pressure coupled systems explode

Hey, I'm still working on the system where I pull two flexible diamod slabs in opposite direction and study the distance dependent speed of the water in between. I attached the mdp file below. The system is scaled extremely in z and pressure looks wrong as well (see attached graph of both). There

[gmx-users] No default Proper Dih. types

hi, I am simulating a protein complex. The peptide in the complex has PRO at the N-terminal. I run pdb2gmx and choose PRO-NH as the cap for the respective N-terminal. pdb2gmx_4mpi -f xyz.pdb -o -ter -ignh -o conf.gro Select N-terminus type (start) 0: PRO-NH2+ 1: PRO-NH 2: NH3+ 3: None 1 N-t

RE: [gmx-users] trjcat xtc files

You should use the -settime option, I think it should solve your problem. Tom --On Monday, November 02, 2009 00:21:31 -0800 Payman Pirzadeh wrote: Your second guess is correct! I used grompp to restart (I had thought it might provide me with the chance to change things if needed). I was sur