RE: [Fwd: Re: [gmx-users] mdrun CVS version crashes instantly when run across nodes in parallel]

> Date: Tue, 22 Jan 2008 20:15:03 +0100 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: [Fwd: Re: [gmx-users] mdrun CVS version crashes instantly when run > across nodes in parallel] > > Hi Erik, > > I have made a test with today's C

[gmx-users] potential tables not working

Hello all, I am trying to learn to use tabulated potential in GROAMCS for defining my own potential. For learning purposes I have created a pdb of silicon atoms of 28 atoms. I want to create two groups each of which will interact in a different way . The gro file is GRowing Old MAkes el Chrono Sw

[gmx-users] Is there any chance to concatenate (fast) more than 1000 energy files....(Solved!!!)

Thanks to Enry, Justin and Mark. As you told me the best way to do the concatenation is : eneconv *.edr -o outfile.edr. -- Sergio Garay Facultad de Bioquimica y Cs. Biológicas Santa Fe (3000) Argentina Casilla de Correo ___ gmx-users mailing list

RE: [Fwd: Re: [gmx-users] mdrun CVS version crashes instantly when run across nodes in parallel]

Hi Carsten and Berk, Your fixes did the trick. Man, there is some great scaling on the CVS version now! Thanks a lot for the help! / Erik ons 2008-01-23 klockan 09:20 +0100 skrev Berk Hess: > > > > > Date: Tue, 22 Jan 2008 20:15:03 +0100 > > From: [EMA

Re: [gmx-users] How to remove H atom from residue in gro file?

Dear All, Just to confirm what Justin said, my MD worked flawlessly with his ffG43a1p files. The only issue was that I had to change my pr.mdp and md.mdp files, following a suggestion I found here: I changed the T coupling groups to "Protein" and "Non-Protein" (I am using the same temperature for t

[gmx-users] comm_grps

Dear All, I am a little confused with the application of comm_grps. I have a lipid-peptide system in which I am using the default values i.e. comm_mode: linear nstcomm: 1 comm_grps: whole system Is there something wrong with defining comm_grps = whole system for the lipid-peptide case? Is it ne

[gmx-users] installation problem for MAC OS

Dear all, I have difficulties when I try to install Gromacs 3.3.2 in my MAC OS. Please see the following for details. configuration: $ ./configure CC=icc CXX=icc F77=ifort --prefix=/Users/yunan/usr/local/Gromacs --with-qmmm-cpmd --with-fft=fftw3 CLAGS=-no-multibyte-chars CPP=/usr/bin/cpp Syst

Re: [gmx-users] installation problem for MAC OS

Hello! A quick fix so that you will be able to compile, is to try to run the configure script with the flag --disable-ia32-sse. Hopefully you should get a working installation, but with no sse- support (which might be what you want :-) Cheers /Per 23 jan 2008 kl. 14.24 skrev Yunan Yan:

Re[2]: [gmx-users] Virtual site and constraints

OK, could I add "dummy mass" that has coordinates and mass such as carbon to keep right moment of inertia? I mean something like this: [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 opls_279 1FMT H 1 0.22 1.008 2 opl

Re: [gmx-users] Virtual site and constraints

Нилов Дмитрий wrote: OK, could I add "dummy mass" that has coordinates and mass such as carbon to keep right moment of inertia? I mean something like this: [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 opls_279 1FMT H 1 0.22

[gmx-users] deshuf.ndx doesn't work for forces?

Hello All, I found sth like a bug regarding the deshuffle index file. I did a simulation using multiple cpus and -sort -shuffle options. After that I tried to use the deshuf.ndx file to recover the original atom order for my trr file by trjconv -n deshuf.ndx ... command. But by checking the out

Re: [gmx-users] polyatomic ion additon by genion

I tried with genbox option with perticular concentration i.e. perticular number of each component like guanidium ion thiocynate ion & water molecule. But while doing PR(position restrain MD) it showing errors : constraints errors in algorithm shake at step 0. t=o.oo ps : water molecule starting at

Re: [gmx-users] deshuf.ndx doesn't work for forces?

LuLanyuan wrote: > Hello All, > I found sth like a bug regarding the deshuffle index file. I did a simulation > using multiple cpus and -sort -shuffle options. After that I tried to use the > deshuf.ndx file to recover the original atom order for my trr file by trjconv > -n deshuf.ndx ... comman