[gmx-users] ACPYPI announcement

Hi List! Well, it's a modest contribution and not properly released but I guess people may find it useful. So 'svn update' and check the website: http://code.google.com/p/acpypi/ often for any eventual update. It's ACPYPI, a tool based on Python to use Antechamber to generate topologies for che

[gmx-users] OPLS parameters for phospho-tyrosine

Dear All, Has anyone a topology for phosphorylated tyrosine residue in OPLS that can be shared? Sincerely, -Maria -- -- Maria G. Technical University of Denmark Copenhagen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/m

[gmx-users] g_rmsf

Hi, I would like to calculate B-factor of protein, so I performed command like this g_rmsf -f .xtc -s .tpr -res -o fluctuate.xvg -od devi.xvg it has run without error.Now i am bit doubting that which .xvg file have to take for plot B-factor values? B-factor is nothing but thermal devat

[gmx-users] deprotonated cys

But of course then you also need to parameterize it, which is not a trivial task. OPLS does not have parameters for a cys thiolate; I'm not sure about other ff's. If you go back to the opls paper, you can follow the route by which they parameterized other ionized sc's. I have been considering d

[gmx-users] settle issue

Dear All, When I try to simulate TIP4Pew water box at 298K, and found the density got from gromacs is relative low (983 g/cm3) than the amber (sander) version 994 g/cm3. I cannot find the reason. The parameters for the tip4pew model are identical. When I check some intra-molecular distances, and se

Re: [gmx-users] settle issue

Mu Yuguang (Dr) wrote: Dear All, When I try to simulate TIP4Pew water box at 298K, and found the density got from gromacs is relative low (983 g/cm3) than the amber (sander) version 994 g/cm3. I cannot find the reason. The parameters for the tip4pew model are identical. When I check some intra-mo

[gmx-users] AFM: .pdo output format

Dear All, I am using pull code to perform AFM on some protein. My pull dimensions are pulldim as Y Y Y for x,y and z coordinates. the output .pdo files are generated, and as far as I have understood, it will get the .pdo output as: time (t), position of ref group (xr,yr,zr), position of pulled

[gmx-users] What's the default pbc of Gromacs trajectories?

Hello, I just noticed the -pbc option for the trjconv command had changed after a version 3.3.x. The original -pbc inbox option were replaced by -pbc atom, -pbc mol etc. As I remember for early versions of Gromacs the default pbc of output trajectories was "whole", which means no broken molecule

Re: [gmx-users] What's the default pbc of Gromacs trajectories?

LuLanyuan wrote: Hello, I just noticed the -pbc option for the trjconv command had changed after a version 3.3.x. The original -pbc inbox option were replaced by -pbc atom, -pbc mol etc. As I remember for early versions of Gromacs the default pbc of output trajectories was "whole", which mean

Re: [gmx-users] g_rmsf

sudheer babu wrote: Hi, I would like to calculate B-factor of protein, so I performed command like this g_rmsf -f .xtc -s .tpr -res -o fluctuate.xvg -od devi.xvg it has run without error.Now i am bit doubting that which .xvg file have to take for plot B-factor values? I think

RE: [gmx-users] What's the default pbc of Gromacs trajectories?

Thanks for your reply. I just checked the online manual for .mdp. But I didn't find an option to change output pbc types. If I need the output trr file to be "whole" as that from an older version, can I set it up anywhere? I understand I can use trjconv to convert trr files. But usually trr f

Re: [gmx-users] What's the default pbc of Gromacs trajectories?

LuLanyuan wrote: Thanks for your reply. I just checked the online manual for .mdp. But I didn't find an option to change output pbc types. If I need the output trr file to be "whole" as that from an older version, can I set it up anywhere? What you are probably seeing is a visualization art