Re: [gmx-users] LINCS warnings generated in NPT ensemble and not in NVT

Lee Soin wrote: Hello! I'm using COM pulling with distance constraint between two domains of a protein. The energy minimization and a 100-ps equilibrating process in the NPT ensemble with position restraints on protein atoms all passed OK. Then I applied a distance constraint between COM of tw

[gmx-users] questions regarding Replica Exchange

 Hi, I have few queries regarding Replica Exchange MD. 1) I have 17 replicas , and the files are named as md_0.trr,..,.md_16.trr.Replica exchange is attempted every 100ps. Thus starting from 0, upto 100ps, the coordinates, velocities etc. that are written in md_0.trr files corresspond

Re: [gmx-users] questions regarding Replica Exchange

sarbani chattopadhyay wrote: Hi, I have few queries regarding Replica Exchange MD. 1) I have 17 replicas , and the files are named as md_0.trr,..,.md_16.trr.Replica exchange is attempted every 100ps. Thus starting from 0, upto 100ps, the coordinates, velocities etc. that are written

Re: [gmx-users] LINCS warnings generated in NPT ensemble and not in NVT

The difference between "restraints" and "constraints" is indeed something I'm aware of :-) Even though distance restraint between COM of two domains worked just OK for me, I would prefer to use distance constraint since that will introduce fewer artifacts and can fix the distance between two domain

[gmx-users] define atoms

Dear mark excuse me. I attempt it again.in analysis result of md peptide I have the table t consist of atoms number column and the other column rmsd(nm).I want to know what is thename of atom which define number 12 in backbone group ?Is it NCC for example related to ser or another aminoacid

Re: [gmx-users] Release of R.E.D. Server

Quoting Joe Joe : What about use for commercial purposes? So far, commercial users can use the R.E.D.-III.2 tools which are distributed in the standalone version. A specific license agreement has to be signed in this case. regards, Francois On Thu, Apr 9, 2009 at 1:31 AM, FyD wrote:

Re: [gmx-users] define atoms

shahrbanoo karbalaee wrote: Dear mark excuse me. I attempt it again.in analysis result of md peptide I have the table t consist of atoms number column and the other column rmsd(nm).I want to know what is thename of atom which define number 12 in backbone group ?Is it NCC for example relat

Re: [gmx-users] Re: Free energy with Gromacs.

You may also want to look at www.alchemistry.org, as it has some general information about how these should be set up. On Wed, Mar 18, 2009 at 8:02 PM, Justin A. Lemkul wrote: > > Again, *please keep all Gromacs-related correspondence on the mailing list* >  The type of information that you have

[gmx-users] Pressure Coupling Problem

Alright, sorry that I wasn't able to help. I'm confused by some apparent contradictions in your posts and I'm not sure that I'm going to be useful to you here. Quoting http://www.gromacs.org/pipermail/gmx-users/2009-April/041173.html: "No matter how much minimization I do the volume of th

[gmx-users] Query

Hi, i am running MD on a system where a protien and a small peptide chain are placed closely. After running the simulation when i was analyzing the system, i got a rmsd plot with numerous bumps. For creating the xtc file i tried different options like -pbc nojump/whole etc and also -center tric,

Re: [gmx-users] Pressure Coupling Problem

I finally figured it out. I went through every parameter step by step and it turns our I had epsilon-r set to 80. Not sure why I had that. Wish gromacs would have given me a warning (hint hint). That explains why my P.E. was 10^-5 instead of 10^-6. Thanks everyone for trying!!!. Sometime the most o

[gmx-users] What's the max number of pull groups?

Hello, Could anyone tell me what the maximum number of COM pulling groups is in GMX 4? Thanks very much. Lanyuan Lu _ MSN 表情魔法书，改变你的对话时代！ http://im.live.cn/emoticons/___ gmx-users mailing

RE: [gmx-users] What's the max number of pull groups?

Hi, There is no maximum. Berk From: lulany...@msn.com To: gmx-users@gromacs.org Date: Fri, 10 Apr 2009 16:04:18 -0400 Subject: [gmx-users] What's the max number of pull groups? Hello, Could anyone tell me what the maximum number of COM pulling groups is in GMX 4? Thanks very much. Lanyu

RE: [gmx-users] What's the max number of pull groups?

Thanks so much, Berk. I have another question regarding the pull code. Can I define a pull group that contains more than one molecules? I tried to define some lipid molecules as a single pull group and pull them out of a bilayer. But I couldn't see the lipids out. If I try one lipid as a pull g

Re: [gmx-users] Problems with Jacobi diagonalization

Dayle Smith wrote: Thanks for your help, Justin. I ran gmxcheck -c topol.tpr ("12284 atoms in file") and gmxcheck -f traj.xtc ("# Atoms 29"). The difference is the SOL atoms. I made another .tpr file with xtcgroups = TDR SOL, and now gmxcheck shows that the number of atoms in topol.tpr is 12

[gmx-users] mdrun_mpi error Signal: Segmentation fault

I have segmentation fault error while running mdrun_mpi( gromacs 4.0.4). I have installed gromacs 4.0.4 two month ago and been working fine. Today, I just got Segment errors. Rebooting does not much help. Here is log: [rd:06790] *** Process received signal *** [d:06790] Signal: Segmentation fault

Re: [gmx-users] mdrun_mpi error Signal: Segmentation fault

nam kim wrote: I have segmentation fault error while running mdrun_mpi( gromacs 4.0.4). I have installed gromacs 4.0.4 two month ago and been working fine. Today, I just got Segment errors. Rebooting does not much help. Here is log: [rd:06790] *** Process received signal *** [d:06790] Signal:

[gmx-users] x2top: duplicate bond, angle, & dihedral parameters; missing VdW parameters

Dear All, I ran the x2top command and successfully generated a topology. However, the topology file has duplicate bond, angle, and dihedral parameters and missing Van der Waals parameters. I am including sections of my topology file for your perusal. Please let me know why this is occurring and ho

[gmx-users] Replica Exchange Error

Hi All, I get the following error when running replica exchange. I have 32 replica's with each replica running on 4 processors (128 total). How do I decrease the domain decomposition cell size, -dss? What should I set it to? Thanks, Ilya DD cell 2 0 0: Neighboring cells do not have atoms: 22217

Re: [gmx-users] Replica Exchange Error

Joe Joe wrote: Hi All, I get the following error when running replica exchange. I have 32 replica's with each replica running on 4 processors (128 total). How do I decrease the domain decomposition cell size, -dss? What should I set it to? You're getting some hints from mdrun, I'd start

Re: [gmx-users] Replica Exchange Error

How do I determine what those values should be? How does it affect the simulation? thanks, Ilya On Fri, Apr 10, 2009 at 8:00 PM, Justin A. Lemkul wrote: > > > Joe Joe wrote: > >> Hi All, >> >> I get the following error when running replica exchange. I have 32 >> replica's with each replica runn

[gmx-users] problem in insertion of protein into lipid bilayer in proper orientation

Dear justin Thanks for tutorial on membrane protein simulation . I am following your tutorial, everything is fine but problem came in concatanation . After orrienting the protein by using editconf I did the concatanation process everything is fine but the file which I got aft

Re: [gmx-users] x2top: duplicate bond, angle, & dihedral parameters; missing VdW parameters

darre...@ece.ubc.ca wrote: Dear All, I ran the x2top command and successfully generated a topology. However, the topology file has duplicate bond, angle, and dihedral parameters and missing Van der Waals parameters. I am including sections of my topology file for your perusal. Please let me know