[gmx-users] Re: Problems with the file 2J3Q.pdb and residue 'TFL'

Captain_Gray wrote: Dear sirs, I'am trying to use the file 2J3Q.pdb (downloaded from your protein bank) with the program Gromacs 3.3.2, and I have great problem, after inputting a command: pdb2gmx -f 2J3Q.pdb -water spc -ignh I receive a fatal error: Residue 'TFL' not found in residue topology d

[gmx-users] free energy calculations in charged systems

Hi all, i am working in polyelectrolyte solutions, and i would like to calculate the free energy for the polyectrolyte system (charged) to change to a neutral (non-charged) system. The question is if it feasible to use the PME electrostatics in gromacs for the above free-energy calculation.

RE: [gmx-users] Compiling GROMACS with FORTRAN?

Howdy Ivano, Would you mind sharing the steps used to compile Gromacs on the BlueGene/L? I've tried this several times with the IBM cross compilers and always end up failing. Thanks for any information, Mike -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf

Re: [gmx-users] MPI configure "cannot compute sizeof (int)"

Thanks Mark. OK I'll concede that the Cray XT3 is a strange bird -- "cc" and "ftn" build a binary for the compute pool only. That binary (serial or parallel) will not run on the front-end but only on the back-end with a "yod" to push it back there. If it checked the size of an int with $CC then

Re: [gmx-users] How to specify .mdp file for position restrained simulation?

jantonioms J. A. Mondragon S wrote: you need to run genpr to generate a restrained position file posresfile.itp with a determined force constant value fc and include the name file in *.mdp file using define label, for example, run genpr -f my_molecule.pdb -o posresfile.itp -fc 20 edit *.mdp to

Re: [gmx-users] problem using makehole grompp

nur avneet wrote: Sir I installed the makehole program as given in instructions, by making a separate copy of gromacs and then added the makehole tar file to it. Then followed the normal steps for installation. But when i set the mdp file as given in tutorial and try to give the grompp comma

Re: [gmx-users] How to specify .mdp file for position restrained simulation?

you need to run genpr to generate a restrained position file posresfile.itp with a determined force constant value fc and include the name file in *.mdp file using define label, for example, run genpr -f my_molecule.pdb -o posresfile.itp -fc 20 edit *.mdp to include cpp = /usr/bin/cpp . . . defi

Re: [gmx-users] Laptop switches off when running GROMACS

David van der Spoel wrote: Sergio de Alencar wrote: Hello there folks, I have been trying to run GROMACS on my laptop, but around 15-20 mins after mdrun starts to run the laptop suddenly switches off. I run it on Red Hat Linux. I'd like to know if anyone has had the same problem and what I

Re: [gmx-users] problem using makehole grompp

On Tue, 20 Nov 2007 11:49:05 + (GMT) nur avneet <[EMAIL PROTECTED]> wrote: Sir I installed the makehole program as given in instructions, by making a separate copy of gromacs and then added the makehole tar file to it. Then followed the normal steps for installation. But when i set th

Re: [gmx-users] g_sas with 3.3 and 3.3.2 gives different results

Isabella Daidone wrote: Hi, I have a box with multiple peptides in it. When I run g_sas either on a single peptide or on all peptides I get different results with version 3.3 and version 3.3.2 1) On a single peptide (I chose 1 peptide for surface calculation and 1 peptide as the output):

[gmx-users] g_sas with 3.3 and 3.3.2 gives different results

Hi, I have a box with multiple peptides in it. When I run g_sas either on a single peptide or on all peptides I get different results with version 3.3 and version 3.3.2 1) On a single peptide (I chose 1 peptide for surface calculation and 1 peptide as the output): with 3.3: # g_sas -f ../t

Re: [gmx-users] Laptop switches off when running GROMACS

Sergio de Alencar wrote: Hello there folks, I have been trying to run GROMACS on my laptop, but around 15-20 mins after mdrun starts to run the laptop suddenly switches off. I run it on Red Hat Linux. I'd like to know if anyone has had the same problem and what I could do to solve it. Maybe

[gmx-users] Laptop switches off when running GROMACS

Hello there folks, I have been trying to run GROMACS on my laptop, but around 15-20 mins after mdrun starts to run the laptop suddenly switches off. I run it on Red Hat Linux. I'd like to know if anyone has had the same problem and what I could do to solve it. Thanks a lot Sergio -- Sérgio de Al

[gmx-users] problem using makehole grompp

Sir I installed the makehole program as given in instructions, by making a separate copy of gromacs and then added the makehole tar file to it. Then followed the normal steps for installation. But when i set the mdp file as given in tutorial and try to give the grompp command, it does no

Re: [gmx-users] How to specify .mdp file for position restrained simulation?

A side note to -DPOSRES, it is actually a C preprocessor defined variable. There is a corresponding #ifdef POSRES ... #endif in the topology file you built. It is default to POSRES, but you can rename it to other name and change accordingly the "define=.." line in the mdp file. Also, you can

Re: [gmx-users] Why so many energy minimization and position restrained simulation steps?

Hi Peggy, To understand the differencxes between the runs, you'll have to read and compare the .mdp files well. I'd suggest to start with the Gromacs manual, chapter 7. For one, position restraint MD depends on the presence of [ position_restraints ] in the topology and has nothing to do with the

Re: [gmx-users] How to specify .mdp file for position restrained simulation?

Hi Use the following term in your mdp: define = -DPOSRES Now, everything is true, depending on the question you ask and the point you're standing... What you may mean is the following: POSRES-Sims are mostly (not always) used for equilibrating the solvent around the protein

Re: [gmx-users] How to specify .mdp file for position restrained simulation?

Peggy Yao wrote: Hi, How to specify the .mdp file in order to run position restrained simulation? From the examples I found on the internet, it seems that the only difference between the .mdp file for position restrained simulation and the one for actual MD simulation is the simulation time -- t

Re: [gmx-users] Why so many energy minimization and position restrained simulation steps?

Peggy Yao wrote: Hi, I am new to Gromacs. I am following this tutorial: http://www.nmr.chem.uu.nl/~abonvin/tutorials/MD-Data/index.html. My question is: why it has multiple steps of energy minimization and position restrained simulation? Is that a common practice? What's the key difference among

Re: [gmx-users] interaction energy of bulk TIP3P

sandeep somani wrote: i see. i reran the trajectory with reaction field electrostatics and that gave a more negative energy value which was closer to what i was expecting. i guess the missing reciprocal space contributions explains this discrepancy. is there a way to get the full interactio

Re: [gmx-users] Creating .ndx for TIP5Pwater

JMandumpal wrote: Dear David, I didn't get the desired box length when I tried to use editconf command ( I took the tip5p box from gromacs/tutor directory) . Then, I tried editconf command to generate .gro file using myown water box. It worked!! I'll bet my car that you did something wrong