Re: [gmx-users] error in umbrella sampling tutorial

http://lmgtfy.com/?q=There+is+a+dangling+bond+at+at+least+one+of+the+terminal+ends.+Fix+your+coordinate+file%2C+add+a+new+terminal+database+entry+(.tdb)%2C+or+select+the+proper+existing+terminal+entry . On Thu, Apr 23, 2015 at 8:47 AM, Ayesha Fatima wrote: > Dear Justin, > I am learning to use t

Re: [gmx-users] CNT going out of the simulation box after NVT.

Use position restraints , or freeze the CNT during the NVT dynamics. On Wed, Mar 4, 2015 at 11:33 PM, soumadwip ghosh wrote: > Dear users, >I am simulating swCNTs in the presence of nucleic acids > with finite

Re: [gmx-users] MD run failed..

Exactly. The reason I asked On Fri, Feb 20, 2015 at 1:14 PM, Justin Lemkul wrote: > > > On 2/20/15 1:01 PM, HANNIBAL LECTER wrote: > >> Just out of curiosity what does -0.1 actually mean? >> >> > It means someone made a mistake :) It's not physically s

Re: [gmx-users] MD run failed..

Just out of curiosity what does -0.1 actually mean? On Fri, Feb 20, 2015 at 8:48 AM, Justin Lemkul wrote: > > > On 2/20/15 6:51 AM, Kalyanashis Jana wrote: > >> Dear all, >> I am doing an MD simulation of a protein system. Energy minimization step >> has been completed smoothly but the position

Re: [gmx-users] Regarding DSSP

Yes, the binary is working on a single pdb file. On Mon, Feb 16, 2015 at 7:06 PM, Justin Lemkul wrote: > > > On 2/16/15 6:55 PM, HANNIBAL LECTER wrote: > >> Sorry, yes, I actually made a copy and pasted in the /usr/bin directory as >> well. So there IS actually a

Re: [gmx-users] Regarding DSSP

: > > > On 2/16/15 6:40 PM, HANNIBAL LECTER wrote: > >> Okay. what can be possibly wrong? I mean if someone CAN run Gromacs-5.0.4 >> + >> DSSP 2.0.4, it should be running in other systems as well unless I am >> messing something up. So I list my steps. >>

Re: [gmx-users] Regarding DSSP

;> Gromacs version? >> >> > DSSP 2.0.4 works with GROMACS 5.0.4 for sure (I ran it just the other > day), but in principle any 2.x version should work with GROMACS 4.6 or > newer (the issue was closed 3 years ago, with minimal reported issues and > no code modifications s

Re: [gmx-users] Regarding DSSP

much. Does anyone know of a version of DSSP executable corresponding to a working Gromacs version? On Mon, Feb 16, 2015 at 4:12 PM, Justin Lemkul wrote: > > > On 2/16/15 4:07 PM, HANNIBAL LECTER wrote: > >> Thanks for your reply. Couple of things. >> I don't really know w

Re: [gmx-users] Regarding DSSP

cs. On Feb 16, 2015 3:45 PM, "Justin Lemkul" wrote: > > > On 2/16/15 3:15 PM, HANNIBAL LECTER wrote: > >> Thanks Justin. So as I mentioned, I am using Gromacs-4.5.6 and there is >> not >> a scope to specify using the -ver command in this particular

Re: [gmx-users] Regarding DSSP

Thanks Justin. So as I mentioned, I am using Gromacs-4.5.6 and there is not a scope to specify using the -ver command in this particular version as opposed to the newer versions (5.0.4). By '' I meant do_dssp -f prot.xtc -s prot.tpr. How do I specify a dssp version in gromacs-4.5.6? Secondl

[gmx-users] Regarding DSSP

Hello all: I am not really sure, what are the various compatibility issues between the do_dssp program of different Gromacs versions and the versions of the DSSP program itself. I am trying to use dssp 2.0.4 and Gromacs 4.5.6. I have used export DSSP=/usr/bin/dssp and then do_dssp - I am

Re: [gmx-users] Problem with Lysozyme in Water Tutorial

It just means you either missed grompp "-f ions.mdp" ... OR the ions.mdp file is not there in the directory where you are performing your simulations. On Mon, Feb 2, 2015 at 12:10 PM, Stephen P. Molnar wrote: > I have installed v-5.0.4 in Debian Wheezy without any warning or erroe > messages.

Re: [gmx-users] Umbrella Sampling Results and Issues

Another simulation between the third and the fourth replica and you should be fine. I don't think what you are observing is an artifact of insufficient sampling time. On Mon, Nov 24, 2014 at 1:03 PM, Agnivo Gosai wrote: > Dear Users > > I am doing an umbrella sampling MD to calculate the binding

Re: [gmx-users] use of Walls in Martini simulations

What about electrostatics? Ewald summation is probably the culprit here. On Oct 24, 2014 12:05 PM, "Ramon Reigada" wrote: > Hi, > > I would like to post a question about simulating with "Walls" in gromacs > and using the Martini force field. > The question is very simple. I am trying to simulate

Re: [gmx-users] gromacs

Do you know why are you even performing MD Simulation? Do you even know what it means? Do you know what to expect? On Thu, Jul 31, 2014 at 1:16 AM, Meenakshi Rajput wrote: > hi gromacs users > I have done the whole mdrun simulation of my protein human serum albumin > complex with ligand and i g

Re: [gmx-users] Hamiltonian Replica Exchange

I would think of using Replica Exchange with Solute Tempering in this case. Look at the paper as to how one can implement this in Gromacs (doi: 10.1002/jcc.21703). Without having more details I would suggest to you to scale the Hamiltonian of each replica such that the Helix bundles are always cor

Re: [gmx-users] (no subject)

You should provide with more information. The error message clearly states that there are multiple definitions for the moleculetype CU1. You should check carefully for redundancies in the top file On Wed, May 21, 2014 at 2:57 AM, Meenakshi Rajput wrote: > dear gromacs users > I tried to add ions

Re: [gmx-users] Nanoparticle topology

Parameters for metals are readily available in various forcefields in Gromacs. If your nanoparticles are gold spheres suspended freely in the system, then you can just get the parameters from from the forcefield files and specify the number of gold atoms in the topology file. On Wed, May 21, 2014

Re: [gmx-users] 答复: about exchange replica with replicas 140

Did you check the .err file as well? What does it say? How many cores do each node in the HPC have? There might be some issues with the supercomputer that you may be using? One of the nodes might have some issues which is probably causing the problem? I have used > 300 cores for replica exchange