Re: [gmx-users] Chain merging problem (pdb2gmx)

hi, On Tuesday 25 April 2006 22:28, Ashutosh Jogalekar wrote: Hello I have three peptide strands with the sequence HHQALVFFA. I am trying to create a .gro file of these. But I don' want to merge these chains together, as the N termini are not capped (NH3+) When I do pdb2gmx, even when I am

Re: [gmx-users] Gromacs-3.3.1 installation

Hi,You should never install software in the same directory as where you are building in, in particular when it is configured with GNU tools.Cheers,ErikOn Apr 26, 2006, at 9:27 AM, Akshay Patny wrote: Hi  I am trying to install Gromacs-3.3.1 The machine is SGI Altix and the output of the uname

Re: [gmx-users] Gromacs-3.3.1 installation

hi, On Wednesday 26 April 2006 09:27, Akshay Patny wrote: Hi I am trying to install Gromacs-3.3.1 The machine is SGI Altix and the output of the uname -a for machine is: Linux redwood 2.6.5-7.244-sn2 #1 SMP Mon Dec 12 18:32:25 UTC 2005 ia64 ia64 ia64 GNU/Linux I do not have root

[gmx-users] Gromacs-3.3.1 installation

Hi I now tried to install gromacs in a separate directory and not the source tree which is: /work1/r0914/gromacs/ I got following error while Make cc -DHAVE_CONFIG_H -I. -I. -I../../../src -I/usr/X11R6/include

Re: [gmx-users] Gromacs-3.3.1 installation

Akshay Patny wrote: Hi I now tried to install gromacs in a separate directory and not the source tree which is: Make sure you do make clean (or maybe make distclean, not sure, try the former first) before the new ./configure Mark ___ gmx-users

[gmx-users] LINCS Error in Gromacs-3.3.1 in pr simulation

Dear all, I have been trying to simulate various mutant models (single mutant) of a enzyme. I am successfully finished simulation of 3 variants including wild type (So for finished up to position restraints of all variants). In one mutation involving Ala in requsite

[gmx-users] Coul-LR in PME and in Reaction Field

Hi everybody! Some more electrostatic questions, if I may.. 1) I think I understood the meaning of the coul-LR term now, but would like to be sure.. The Coul-LR term is only printed in PME runs if rcoul rlist. In PME, coul-LR would be the (short range) real sum term computed between rlist and

RE: [gmx-users] comm-mode = Angular

Hi Tsjerk, I have been wondering whether Andrea Amadei and coworkers' method ( J. Chem. Phys. 112(1) pp. 9-23)has beenimplemented in Gromacs yet. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265

Re: [gmx-users] comm-mode = Angular

Hi Abu,In fact, I have it implemented in two versions (3.1.4 and 3.2.1), but haven't contributed it to the official code yet. At this point I don't have the time either :S However, you can download my versions at http://md.chem.rug.nl/~tsjerk/GMX/Cheers,TsjerkOn 4/26/06, Naser, Md Abu [EMAIL

Re: [gmx-users] comm-mode = Angular

Hi Abu,Indeed. You have to add a parameter rototr = yes. Note that the changes in the .tpr file make it impossible to use these .tpr with other versions of gromacs and vice versa. Besides, you need a reference structure for the removal of the rotation/translation. This file has a fixed name:

[gmx-users] Benching against different compilers - Help needed

Hi all. Well, some time ago I decided to bench gromacs on AMD64 machines compiled with different compilers (both single and double precision, both internal and external blas and lapack, just FFTw 3 for fourier) in order to see which one performs better. To time, I have available GCC, PGI and

Re: [gmx-users] error while running Energy minimisatio mdrun

I could only tell you the same problem met by myself. First, it happened as you described. I checked everyting concerned. But nothing seemd abnormal . At last, I changed the node of cluster on which i performed EM. Then, you know, it works well. I guess that maybe it also relates to the

[gmx-users] gromacs installation on True64 Unix system

Dear Gmx-users, I am trying to install the double precision of gromacs (3.3.1) on a True64 Unix system. However, there is always an error during the precess of compiling. Here is the tail of the config.log: #define PACKAGE gromacs #define PACKAGE_BUGREPORT gmx-users@gromacs.org #define

[gmx-users] afm pulling

Dear all, I am simulating an unbinding process with the pull code (afm option). I've been reading previous posts about this option and I just wanted to clarify some ideas and ask some questions. There are: 1-The pulling can be done choosing two different molecules. Why a particular group within

[gmx-users] 3.3.1 installation on True64 Unix system

Dear GMX-users, Here are the script I used to install the GROMACS-3.3.1 double precision on a True64 Unix system. I installed fftw-3.0.1 first and it was successful. ./configure --enable-float --enable-type-prefix; make; make install ./configure --enable-type-prefix; make; make install Then I

Re: [gmx-users] afm pulling

Hi, Dear all, I am simulating an unbinding process with the pull code (afm option). I've been reading previous posts about this option and I just wanted to clarify some ideas and ask some questions. There are: 1-The pulling can be done choosing two different molecules. Why a particular group