[gmx-users] Error compiling Gromacs 4.5.4: "relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC"

the only issue is with 4.5.4. The system is running Scientific Linux 5.5. $ uname -a Linux ST-HPC-Main 2.6.18-128.7.1.el5 #1 SMP Mon Aug 24 08:12:52 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux I am puzzled as to why it doesn't work in 4.5.4 but did until the previous release. Did something

Re: [gmx-users] doubt in mdrun

Dr. Pablo Englebienne Postdoctoral Researcher *TU Delft / 3mE / Process & Energy* /Engineering Thermodynamics (ETh) group/ Building 46 Leeghwaterstraat 44, room 030 2628 CA Delft The Netherlands *T* +31 (0)15 27 86662 *E* p.englebie...@tudelft.nl <mailto:p.englebie...@tudelft.nl> On

[gmx-users] g(r) does not go to 1 at long r -- bug in g_rdf?

ssary. Take care, Pablo -- Dr. Pablo Englebienne Postdoctoral Researcher *TU Delft / 3mE / Process & Energy* /Engineering Thermodynamics (ETh) group/ Building 46 Leeghwaterstraat 44, room 030 2628 CA Delft The Netherlands *T* +31 (0)15 27 86662 *E* p.englebie...@tudelft.nl <mailt

[gmx-users] trjconv -pbc nojump across multiple trajectories

nts! Regards, Pablo -- Dr. Pablo Englebienne Postdoctoral Researcher *TU Delft / 3mE / Process & Energy* /Engineering Thermodynamics (ETh) group/ Building 46 Leeghwaterstraat 44, room 030 2628 CA Delft The Netherlands *T* +31 (0)15 27 86662 *E* p.englebie...@tudelft.nl <mailto:p.englebie..

[gmx-users] Re: trjconv -pbc nojump across multiple trajectories

what would be the easiest way to get the last frame out of the trajectory? I can think of using the output of gmxcheck to get the time of the last frame and then use it as the argument to "trjconv -b", but is there a simpler way? Regards, Pablo Dr. Pablo Englebienne Postdoctoral R

[gmx-users] Difficulty building a topology for a synthetic branched PEG-peptide molecule

s "None" yields the same error. Unfortunately, there is nothing about this error in http://www.gromacs.org/Documentation/Errors . Any suggestions on how to make this work will be greatly appreciated! -- Pablo Englebienne, PhD Dept. of Biomedical Engineering Dept. of Chemistry and Chemic

[gmx-users] Re: Difficulty building a topology for a synthetic, branched PEG-peptide molecule [SOLVED]

good question. You would likely not have gotten anywhere giving less detail :) Thanks, it actually helped putting everything in writing, as it pointed out the few things that I hadn't yet looked at in detail... Pablo Englebienne, PhD Dept. of Biomedical Engineering Dept. of Chemistry a

[gmx-users] Improper dihedrals on planar rings

ed to keep a 6-membered ring flat? What about a 6-membered ring represented with united atoms? Thanks for reading so far (and many thanks for replying!). Regards, Pablo -- Pablo Englebienne, PhD Institute of Complex Molecular Systems (ICMS) Eindhoven University of Technology, TU/e PO Box 51

[gmx-users] Chloroform (CHCl3) solvent box for G53a5 force field

ed in AmberTools (amber10/dat/solvents/cform/cform.pdb and chcl3_equil.pdb.1). I took this one and I'm equilibrating it to use it later. In the mean time, I wanted to know if I overlooked something, and there is a CHCl3 box to use with the GROMOS forcefield? Thanks! -- Pablo Englebienne, PhD In

[gmx-users] Re: Chloroform (CHCl3) solvent box for G53a5 force field

I'm trying to simulate a small molecule in a chloroform box using the GROMOS G53a5 forcefield. I realized that the parameters for the solvent are present in the ffG53a5.rtp file, however I could not find a CHCl3 solvent box included in GROMACS. I did find, however, a CHCl3 solvent box equilib

[gmx-users] Re: Chloroform (CHCl3) solvent box for G53a5 force field

OK, I started over with the CHCl3 box from scratch. I prepared the following itp file from the CHCL3 parameters in ffG53a5.rtp: ---[chcl3.itp]--- [ moleculetype ] ; Namenrexcl CHCL3 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1

[gmx-users] Re: Chloroform (CHCl3) solvent box for G53a5 force field

olvent box in production runs? Regards, Pablo -- Pablo Englebienne, PhD Institute of Complex Molecular Systems (ICMS) Eindhoven University of Technology, TU/e PO Box 513, HG -1.26 5600 MB Eindhoven, The Netherlands Tel +31 40 247 5349 ___ gmx-users mailing list

[gmx-users] Re: Chloroform (CHCl3) solvent box for G53a5 force field

ue -2147483631. It should have been within [ 0 .. 84 ] --- I'll appreciate pointers as to what to try next! Regards, Pablo -- Pablo Englebienne, PhD Institute of Complex Molecular Systems (ICMS) Eindhoven University of Technology, TU/e PO

[gmx-users] How to tune number of CPUs for a run?

quest? Besides this, should the PP/PME reported by grompp always fall in the range 0.25-0.33? What if it is lower (e.g., 0.16)? I'm attaching an mdrun logfile of a failed run. Thanks for suggestions, Pablo -- Pablo Englebienne, PhD Institute of Complex Molecular Systems (ICMS) Eindhoven

[gmx-users] Continuous trajectory from trjconv?

n a continuous way? Thanks in advance for reading, and more for replying! Take care, Pablo -- Pablo Englebienne, PhD Institute of Complex Molecular Systems (ICMS) Eindhoven University of Technology, TU/e PO Box 513, HG -1.26 5600 MB Eindhoven, The Netherlands Tel +31 40 247 5349 -- gmx-use

[gmx-users] Re: Continuous trajectory from trjconv?

Thanks Tsjerk, I figured as much, but wanted to make sure I wasn't overlooking something... Take care, Pablo Hi Pablo, You want to mutually exclusive things. That is by definition impossible. Sorry, Tsjerk On Mon, Mar 1, 2010 at 11:02 AM, Pablo Englebienne wrote: Hi, I made an N