Re: [gmx-users] running a crashed run

I have read that document .. but still I do have confusion .. mdrun -s md_0_1.tpr -f md_0_1.trr -e md_0_1.edr -o md_0_1.trr -g md_0_1.log -cpi -append... and I also completed 2 ns of the 3ns simulation.. So I want to whether it will start from 2ns or from beginning... -- Bharat Ph.D. Candidate R

Re: [gmx-users] running a crashed run

On 01/20/11, bharat gupta wrote: > > Hi, >   >   > I was running a simulation for 3ns and the system got turned off some how and > I restarted that crashed run ... will continue from the step at which it got > crashed or will it start from begining again ?? > > This is what the checkpoint

[gmx-users] running a crashed run

Hi, I was running a simulation for 3ns and the system got turned off some how and I restarted that crashed run ... will continue from the step at which it got crashed or will it start from begining again ?? -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laborator

Re: [gmx-users] (no subject)

On 01/20/11, a...@rri.res.in wrote: > Dear gmx users, > > > Can anyone please help me out with the commands used for > finding the pair correlation function of the water molecules > with respect to the C alpha atom of the protein and > reorientational time correlation function of

[gmx-users] (no subject)

Dear gmx users, Can anyone please help me out with the commands used for finding the pair correlation function of the water molecules with respect to the C alpha atom of the protein and reorientational time correlation function of the water.?? regards aish -- gmx-users mailing li

Re: [gmx-users] CNT

On 20/01/2011 10:51 AM, trevor brown wrote: Hi Justin, I added lines to ffnonbonded.itp. It resulted in following error. It has some warnings and an error. I am interested in error. After that I will look at the warnings. In which file we may have an error? It is not specified. best wishes tr

RE: [gmx-users] CNT

The warning is due to having the molecules in the topology .top file listed in a different order to how they appear in the coordinate file, .gro The list within the topology has to be in the same order, even if you have broken up groups of the same molecules in the coordinate file. As for the

[gmx-users] CNT

Hi Justin, I added lines to ffnonbonded.itp. It resulted in following error. It has some warnings and an error. I am interested in error. After that I will look at the warnings. In which file we may have an error? It is not specified. best wishes trevor Generated 335790 of the 335790 non-bonded

Re: [gmx-users] 1-4 interaction between X and Y at distance 1.804 which is larger than 1-4 table size 1.800 nm.

On 20/01/2011 9:53 AM, TJ Mustard wrote: On January 18, 2011 at 12:50 PM Mark Abraham wrote: On 19/01/2011 7:33 AM, TJ Mustard wrote: On January 17, 2011 at 3:48 PM Mark Abraham wrote: On 18/01/2011 10:27 AM, TJ Mustard wrote: On January 17, 2011

Re: [gmx-users] 1-4 interaction between X and Y at distance 1.804 which is larger than 1-4 table size 1.800 nm.

  On January 18, 2011 at 12:50 PM Mark Abraham wrote: On 19/01/2011 7:33 AM, TJ Mustard wrote:   On January 17, 2011 at 3:48 PM Mark Abraham wrote:

[gmx-users] RE: Important: Bugs in NEMD calculation

O); >> >> > >> >> > which would be incorrect for a non-rectangular box. You should however >> >> > use a rectangular box for this kind of calculations, although this is >> >> > not enforced by grompp. >> >> >> >>

[gmx-users] Re: gmx-users Digest, Vol 81, Issue 130

gt; > > > > > > > Xiaohu > > > > * > > > > > > > > > > > > > -- > > > David van der Spoel, Ph.D., Professor of Biology > > > Dept. of Cell & Molec. Biol., Uppsala University. > > > Box 596, 75124 Upps

Re: [gmx-users] CNT

trevor brown wrote: Dear Justin, Regarding our previous discussion under "CNT" topic, you want to know exactly what I did to define C-C interaction. I have summarized it below. 1. I copied oplsaa.ff folder in my working directory 2. I added following lines to atomname2type.n2t Copls_995

RE: [gmx-users] RE: Important: Bugs in NEMD calculation

http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. >

[gmx-users] CNT

Dear Justin, Regarding our previous discussion under "CNT" topic, you want to know exactly what I did to define C-C interaction. I have summarized it below. 1. I copied oplsaa.ff folder in my working directory 2. I added following lines to atomname2type.n2t Copls_9950 12.011 2C

Re: [gmx-users] Dell PowerEdge M710 with Intel Xeon 5667 processor

At the same time, I would emphasize that from a scaling point of view less cores per node is better than lots of cores because processors on the same node share the same network link. Also frequency of CPUs on 2-socket nodes goes higher than 4+-socket configurations. -- Szilárd On Wed, Jan 19, 2

RE: [gmx-users] Important: Bugs in NEMD calculation

> Date: Wed, 19 Jan 2011 20:52:13 +0100 > From: sp...@xray.bmc.uu.se > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Important: Bugs in NEMD calculation > > On 2011-01-19 20.43, Berk Hess wrote: > > > > > > > Date: Wed, 19 Jan 2011 19:13:12 +0100 > > > From: sp...@xray.bmc.uu.se > > >

Re: [gmx-users] Dell PowerEdge M710 with Intel Xeon 5667 processor

On 20/01/2011 3:33 AM, Maryam Hamzehee wrote: Dear Szilárd, Many thanks for your reply. I've got following reply from my question from Linux-PowerEdge mailing list. I was wondering which one applies to GROMACS parallel computation (I mean CPU bound, disk bound, etc). In serial, GROMACS is

[gmx-users] RE: Important: Bugs in NEMD calculation

Biol., Uppsala University. > > Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. > > sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se > > -- > > gmx-users mailing listgmx-users@gromacs.org > > http://lists.gromacs.org/m

Re: [gmx-users] Important: Bugs in NEMD calculation

On 2011-01-19 20.43, Berk Hess wrote: > Date: Wed, 19 Jan 2011 19:13:12 +0100 > From: sp...@xray.bmc.uu.se > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Important: Bugs in NEMD calculation > > On 2011-01-19 18.36, Xiaohu Li wrote: > > Hi, All, > > I've found a bug in the NEMD c

RE: [gmx-users] Important: Bugs in NEMD calculation

> Date: Wed, 19 Jan 2011 19:13:12 +0100 > From: sp...@xray.bmc.uu.se > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Important: Bugs in NEMD calculation > > On 2011-01-19 18.36, Xiaohu Li wrote: > > Hi, All, > > I've found a bug in the NEMD calculation for viscosity. This has > > b

Re: [gmx-users] Important: Bugs in NEMD calculation

On 2011-01-19 18.36, Xiaohu Li wrote: Hi, All, I've found a bug in the NEMD calculation for viscosity. This has been reviewed in /*Hess's paper at JCP 116 209 2002.*/ The version of gromacs I'm using is the development version. Notice that this version correct a previous but of 4.5.3,

[gmx-users] Important: Bugs in NEMD calculation

Hi, All, I've found a bug in the NEMD calculation for viscosity. This has been reviewed in *Hess's paper at JCP 116 209 2002.* The version of gromacs I'm using is the development version. Notice that this version correct a previous but of 4.5.3, where you uses NEMD, both the term V(eq. 21

Re: [gmx-users] Dell PowerEdge M710 with Intel Xeon 5667 processor

Dear Szilárd, Many thanks for your reply. I've got following reply from my question from Linux-PowerEdge mailing list. I was wondering which one applies to GROMACS parallel computation (I mean CPU bound, disk bound, etc).  >There shouldn't be any linux compatibility issues with any PowerEdge  >

Re: [gmx-users] GROMOS96 topology for small molecule

thanks :) 2011/1/19 mohsen ramezanpour > It is on now,you can use it. > as Justin said you should validate it. > best > > > On Tue, Jan 18, 2011 at 9:37 PM, Justin A. Lemkul wrote: > >> >> >> C.Y. Chang wrote: >> >>> Hi, >>> >>> I need to obtain the GROMOS96 topology files (and including the >>

[gmx-users] Re: Contstraints = all-angles

On 2011-01-19 15.56, munu...@yahoo.com wrote: Sir, Please suggest me on how to use the parameter 'Contstraints = all-angles" in the mdp file. M. Baskar Research Scholar Dept. of Biophysics, Panjab Univesity, Chandigarh, India Don't use it at all with LINCS. The LINCS paper explains why not. I

Re: [gmx-users] Re: Problem in Disulfide Bond

parthi...@ncbs.res.in wrote: Hi I am using a dimer for my simulation system which is connected by 2 disulfide bonds. After energy minimization for even few cycles, the disulfide bond breaks which is not expected. Bonds do not break in classical molecular mechanics. One of two things is hap

[gmx-users] Re: Problem in Disulfide Bond

Hi I am using a dimer for my simulation system which is connected by 2 disulfide bonds. After energy minimization for even few cycles, the disulfide bond breaks which is not expected. i have applied amber99 force field and prepared the system. while i tried with another force field in Gromacs whic

Re: [gmx-users] Help with the heme group in forcefield gromos53a6

Tanos Franca wrote: Dear users, We are trying to perform a MD simulation of a protein with a heme group using the gromos53a6 force field but, when trying to run grompp, we receive the error mesage: Program grompp, VERSION 4.0.3 Source code file: ../../../../src/kernel/toppush.c, line: 947 F

[gmx-users] Help with the heme group in forcefield gromos53a6

Dear users, We are trying to perform a MD simulation of a protein with a heme group using the gromos53a6 force field but, when trying to run grompp, we receive the error mesage: Program grompp, VERSION 4.0.3 Source code file: ../../../../src/kernel/toppush.c, line: 947 Fatal error: Atomtype FE

Re: [gmx-users] the final structure

ahmet yıldırım wrote: Dear users, Which the file should I use to visualize (using pymol) the final structure after the simulation finish? The final structure is contained in whatever file you specified with the mdrun -c flag. By default, it is a .gro, which I don't believe PyMOL can han

Re: [gmx-users] the final structure

On 19/01/2011 11:32 PM, ahmet yıldırım wrote: Dear users, Which the file should I use to visualize (using pymol) the final structure after the simulation finish? mdrun -c sets the name of that file, which defaults to confout.gro. That can be understood from the contents of mdrun -h, but the

Re: [gmx-users] the final structure

I believe you have to use the trjconv program. For more details about it, please read [1]. [1] http://manual.gromacs.org/current/online/trjconv.html -- Rodrigo Antonio Faccioli Ph.D Student in Electrical Engineering University of Sao Paulo - USP Engineering School of Sao Carlos - EESC Department

[gmx-users] the final structure

Dear users, Which the file should I use to visualize (using pymol) the final structure after the simulation finish? Thanks -- Ahmet YILDIRIM -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.o

Re: [gmx-users] PRODRG server

mohsen ramezanpour wrote: Dear All I generated toplogy file for a drug by PRODG server. How can I validate it? i looked at these links but there are not a way for doing that. http://www.gromacs.org/Documentation/How-tos/Parameterization http://www.gromacs.org/Downloads/Related_Software/PRODRG#T

[gmx-users] PRODRG server

Dear All I generated toplogy file for a drug by PRODG server. How can I validate it? i looked at these links but there are not a way for doing that. http://www.gromacs.org/Documentation/How-tos/Parameterization http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips thanks in advance -- gmx

Re: [gmx-users] GROMOS96 topology for small molecule

It is on now,you can use it. as Justin said you should validate it. best On Tue, Jan 18, 2011 at 9:37 PM, Justin A. Lemkul wrote: > > > C.Y. Chang wrote: > >> Hi, >> >> I need to obtain the GROMOS96 topology files (and including the >> corresponding PDB files) for some small molecules. >> I cou

Re: [gmx-users] Convert residue coordinates to dihedral angles

On 01/19/11, Adam Bin Idu Jion wrote: > > > > > > > > > > > > > Hi! > >   > > I'm simulating a 10-residue protein. My trajectory files record these > residues in terms of x, y, z coordinates. > > Can Gromacs convert these coordinates into dihedral angles for each residue? > >  

[gmx-users] Convert residue coordinates to dihedral angles

Hi!   I'm simulating a 10-residue protein. My trajectory files record these residues in terms of x, y, z coordinates. Can Gromacs convert these coordinates into dihedral angles for each residue?   For example, Residue 1: SinPhi = 20, Sin Psi =25, Cos Phi = 15, Sin Phi =75 Residue 2: etc .. etc

Re: [gmx-users] Fourier transformation of dipole autocorrelation function

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 01/18/2011 10:56 PM, Mark Abraham wrote: > On 19/01/2011 8:19 AM, Nilesh Dhumal wrote: >> Then didn't mentioned what they calculated Fourier transformation of >> dipole >> autocorrelation. They have given the equations and theory in papers. > > I'd