[gmx-users] wrong string length 0 for string buf

Hi gromacs users When I uesed command : trjconv -f com_full.xtc -s com_full.tpr -n com.ndx -o com.xtc -pbc nojump -ur compact -center gromacs gives me the following error: Program trjconv, VERSION 4.0.5 Source code file: gmxfio.c, line: 609 Fatal error: wrong string length 0 for string buf (so

RE: [gmx-users] wrong string length 0 for string buf

Hi, Your tpr file is probably empty (0 bytes). Berk Date: Sat, 21 Aug 2010 11:54:17 +0330 From: karami.lei...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] wrong string length 0 for string buf Hi gromacs users When I uesed command : trjconv -f com_full.xtc -s com_full.tpr -n com.n

[gmx-users] How to do Energy minimization and MD of protein-new ligand complex

I am new to Gromacs. I have a protein where ligand is bound to it. I got this complex after carrying out docking of ligand to protein.The ligand is new. So no topology and parameter files are available. At first i want to carryout energy minimization of this complex and then I want to find out how

Re: [gmx-users] How to do Energy minimization and MD of protein-new ligand complex

priyabrata panigrahi wrote: I am new to Gromacs. I have a protein where ligand is bound to it. I got this complex after carrying out docking of ligand to protein.The ligand is new. So no topology and parameter files are available. At first i want to carryout energy minimization of this compl

[gmx-users] Calculate observed "Acceptance Ratio" from REMD simulation

Calculate observed "Acceptance Ratio" from REMD simulation Dear Gromacs users, I used the Gromacs how-to [1] to setup a REMD simulation. The targeted acceptance ratio was P_acp=15%, I used the temperature generator web-service [2] to get the temperature spacing. From the test simulation I want to

Re: [gmx-users] Calculate observed "Acceptance Ratio" from REMD simulation

On 2010-08-21 15.05, henri mone wrote: Calculate observed "Acceptance Ratio" from REMD simulation Dear Gromacs users, I used the Gromacs how-to [1] to setup a REMD simulation. The targeted acceptance ratio was P_acp=15%, I used the temperature generator web-service [2] to get the temperature sp

Re: [gmx-users] Calculate observed "Acceptance Ratio" from REMD simulation

- Original Message - From: henri mone Date: Saturday, August 21, 2010 23:06 Subject: [gmx-users] Calculate observed "Acceptance Ratio" from REMD simulation To: gmx-users@gromacs.org > Calculate observed "Acceptance Ratio" from REMD simulation > > Dear Gromacs users, > > I used the

[gmx-users] Error when compiled with fortran compiler in double precision

Dear gmx-users, An error was found when compiled gmx with fortran compiler in double precision, listed in the following: ../../../../../gmx-git/src/gmxlib/nonbonded/nb_kernel_f77_double/nb_kernel_f 77_double.c:141: error: 'nbkernel204_f77_double' undeclared here (not in a function) ../../.

[gmx-users] How to center molecules in the box with trjconv ?

" Hi gromacs users When I uesed command : trjconv -f com_full.xtc -s com_full.tpr -n com.ndx -o com.xtc -pbc nojump -ur compact -center gromacs gives me the following error: Program trjconv, VERSION 4.0.5 Source code file: gmxfio.c, line: 609 Fatal error: wrong string length 0 for string buf (sour

[gmx-users] editying top file after solvation

Dear gmx users, I am solvating a solute with a solvent molecule using command line below: genbox -cp solute.gro -cs solvent.gro -o solvated.gro -p solute.top solute is in a 20nm cubic box and by this command I am getting solvated box. solute.top is the top file of solute. I searched the archive

Re: [gmx-users] editying top file after solvation

jojo J wrote: Dear gmx users, I am solvating a solute with a solvent molecule using command line below: genbox -cp solute.gro -cs solvent.gro -o solvated.gro -p solute.top solute is in a 20nm cubic box and by this command I am getting solvated box. solute.top is the top file of solute. I se