[gmx-users] reg puuling error

Dear Justin thank you for your previous mail When i do Steered MD , During final MD i got the following message in command prompt is it critical error OR may i ignore this message What will i do to avoid this error? I am seeing negative pull rate Pull reference distance for group 1 is negative

Re: [gmx-users] Bond constraints during the equilibration for membrane-protein system

li lv wrote: Dear All I am conducting a MD simulation for membrane protein with GMX 4.0.5. I met lots of LINCS warnings (almost for angle change of N-H and C-H bond) when doing equilibration for the membrane-protein system under NPT condition. I had doing energy minimization (emtol = 500

[gmx-users] Bond constraints during the equilibration for membrane-protein system

Dear All I am conducting a MD simulation for membrane protein with GMX 4.0.5. I met lots of LINCS warnings (almost for angle change of N-H and C-H bond) when doing equilibration for the membrane-protein system under NPT condition. I had doing energy minimization (emtol = 500) before the equilibr

Re: [gmx-users] use AMBER ff03 force field in gromacs 4

On Thursday, May 12, 2011 at 9:03 AM"mirc...@sjtu.edu.cn" wrote:   > I am using GROMACS 4 to do MD simulations of protein-ligand complexes.I > encountered some > problems when generating the topology file of the ligands. I generate the > topology file > of ligands by using topolbuild package.

Re: [gmx-users] index file

ahmet yıldırım wrote: Dear users, Firstly thanks for your replies. I have two ligands as I said before. I will analyze the system together ligands after the simulation is finished. For example: I want to plot potential energy of all system (that is, protein+LİGA+LİGB) by g_energy. This is n

Re: [gmx-users] index file

Dear users, Firstly thanks for your replies. I have two ligands as I said before. I will analyze the system together ligands after the simulation is finished. For example: I want to plot potential energy of all system (that is, protein+LİGA+LİGB) by g_energy. Then, Should I create the groups as th

Re: [gmx-users] Rigid structure and flexible structure present in sing system

wrote: > If you simply want to know how to freeze one structure, then use freeze groups > and energy exclusions without pressure coupling, or use position restraints and > refcoordscaling=com with position restraints, or create an elastic network of > restraints. Is it really not possible (or c

Re: [gmx-users] index file

2011/5/12 Justin A. Lemkul : > > > lina wrote: >> >> make_ndx -f your.gro/pdb -n your.ndx -o your.ndx >> >> LiGA & LİGB: > > This is not correct.  You need to use | rather than &.  Using logical and > (&) means the index group will contain atoms that are common to both LIGA > and LIGB.  If they are

Re: [gmx-users] index file

lina wrote: make_ndx -f your.gro/pdb -n your.ndx -o your.ndx LiGA & LİGB: This is not correct. You need to use | rather than &. Using logical and (&) means the index group will contain atoms that are common to both LIGA and LIGB. If they are distinct entities, the group will be empty.

Re: [gmx-users] index file

make_ndx -f your.gro/pdb -n your.ndx -o your.ndx LiGA & LİGB: q in grompp add -n your.ndx 2011/5/12 ahmet yıldırım : > Dear users, > > I have two ligands. I created a special index group that merges the protein, > LiGA and LİGB. > > I have the pr.mdp file as the following: > ... > energygrps   

Re: [gmx-users] use AMBER ff03 force field in gromacs 4

mirc...@sjtu.edu.cn wrote: Dear All: I am using GROMACS 4 to do MD simulations of protein-ligand complexes.I encountered some problems when generating the topology file of the ligands. I generate the topology file of ligands by using topolbuild package. The atom types of GAFF force field ar

[gmx-users] use AMBER ff03 force field in gromacs 4

Dear All: I am using GROMACS 4 to do MD simulations of protein-ligand complexes.I encountered some problems when generating the topology file of the ligands. I generate the topology file of ligands by using topolbuild package. The atom types of GAFF force field are assigned to the atoms of

[gmx-users] use AMBER ff03 force field in gromacs 4

Dear All: I am using GROMACS 4 to do MD simulations of protein-ligand complexes.I encountered some problems when generating the topology file of the ligands. I generate the topology file of ligands by using topolbuild package. The atom types of GAFF force field are assigned to the atoms o

[gmx-users] Re: CG database for POPC

Du Jiangfeng (BIOCH) wrote: Dear Justin, Thank you for your help. From MARTINI website, I got the POPE files as you said. The next step I think I should change PE into PC manually to make POPC files, is it right? Also, sorry that I didn't post my question Yes, as I said before. in a correct

Re: [gmx-users] Rigid structure and flexible structure present in sing system

Luke Goodsell wrote: Thanks for the response, Justin. Add a [constraints] directive for the molecule you want to make rigid and use "constraints = none" in the .mdp file. Thus, only the bonds manually set to be constraints will be constrained. Great, this is a much better solution than the

[gmx-users] Energy groups

Hi all If I have a topology with set up below (excerpts). And define energy groups in the .mdp file say 'virtsites' and 'endgroup' in correspondence with the index file. Will defining energygrp_exl 'virtsites' and 'endgroup' prevent nonbonding interactions between any atom in either of these grou

[gmx-users] modified PRODRG2 itp file

Dear justin, I couldn't get the paper that you recommended in your Protein-ligand complex tutorial.so I don't know how should I check and assign a charge for unknown group, in the PRODRG2 *.itp file. best regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mail

Re: [gmx-users] Rigid structure and flexible structure present in sing system

Thanks for your response, Chris. > If I read between the lines correctly, you know how to do this in gromacs, > but you wish that you got a big speedup from freezing most of the atoms in > your system. Partly; the only method I knew of was inelegant and likely to cause bizarre outcomes. >If that

Re: [gmx-users] Rigid structure and flexible structure present in sing system

Thanks for the response, Justin. > Add a [constraints] directive for the molecule you want to make rigid and > use "constraints = none" in the .mdp file.  Thus, only the bonds manually > set to be constraints will be constrained. Great, this is a much better solution than the one I knew. > Note

Re: [gmx-users] Arrest

Please do not forward such messages to discussion forums. It doesn't make sense. On Wed, May 11, 2011 at 9:24 PM, wrote: > Hi , > > I just sent a fax to PM, Manmohan Singh and Maharashtra CM, Prithviraj > Chavan asking them to respect public opinion on the Jaitapur issue. > > Please read the mai

Re: [gmx-users] about g_hbond

I got it. I should have outputted the -hbn file. Thanks, On Thu, May 12, 2011 at 1:09 PM, lina wrote: > /* y-label: "Hydrogen Bond Index" */ > > is it relevant to the total number of hydrogen bonds? > > such as > /* XPM */ > /* x-label: "Time (ps)" */ > /* y-label: "Hydrogen Bond Index" */ > /

[gmx-users] Arrest

Hi ,I just sent a fax to PM, Manmohan Singh and Maharashtra CM, Prithviraj Chavan asking them to respect public opinion on the Jaitapur issue. Please read the mail below from Former Chief of Naval Staff of the Indian Navy, Admiral L. Ramdas, and take action. http://greenpeace.in/take-action/stop-