Re: [gmx-users] simulation popc

Hi Jordi et al. Note the ffgmx force field should not be used for production runs. The force field is deprecated. Check the archives for more discussion on that. To use popc in simulation, try to dig up popc parameters for a current force field (like ffG43a1). Tsjerk On 6/12/07, Jordi Camps <[E

Re: [gmx-users] Stuck --> unstuck ...

David van der Spoel a écrit : Stéphane Téletchéa wrote: I've found out where the problem lie (at least one of ...). Small reminder: i've tried to setup a system consisting of HIV protease + one ligand on a water box. I used the excellent protocol from John E. Kerrigan (Drug-enzyme tutorial) i

Re: [gmx-users] Stuck --> unstuck ...

Stéphane Téletchéa wrote: David van der Spoel a écrit : Stéphane Téletchéa wrote: I've found out where the problem lie (at least one of ...). Small reminder: i've tried to setup a system consisting of HIV protease + one ligand on a water box. I used the excellent protocol from John E. Kerrig

[gmx-users] gromacs on IBM Power 5 Linux Machine: Preprocessor problem

Dear All, We have this IBM POWER5 machine with Linux SLES. The FFTW and GROMACS are compiling without any errors (compiler is gcc), but when we are trying to run a job on the machine, its exiting saying "illegal instruction". Looking at the things, it seemed that the cpp it generated is just a dum

Re: [gmx-users] gromacs on IBM Power 5 Linux Machine: Preprocessor problem

Monika Sharma wrote: Dear All, We have this IBM POWER5 machine with Linux SLES. The FFTW and GROMACS are compiling without any errors (compiler is gcc), but when we are trying to run a job on the machine, its exiting saying "illegal instruction". Looking at the things, it seemed that the cpp it g

Re: [gmx-users] gromacs on IBM Power 5 Linux Machine: Preprocessor problem

I am using Gromacs3.3 version, and I was trying grompp for energy minimization, which is not working. Even the mdrun didnt work. The same file seems to work properly on simple Fedora linux PC, but not on IBM Power linux. Dont know then what the problem is?? Mark Abraham wrote: Monika Sharma

[gmx-users] RNA ffgmx.hdb problems

Hello all, as a beginner I try gromacs for the first time. At first my aim is just the energy minimization of a small RNA aptamer. I started to convert my pdb file into a gromacs structure file with pdb2gmx and failed. I obtained this error: Fatal error: Atom H1* in residue GUA 2 not found in rtp

Re: [gmx-users] gromacs on IBM Power 5 Linux Machine: Preprocessor problem

Monika Sharma wrote: I am using Gromacs3.3 version, and I was trying grompp for energy minimization, which is not working. Even the mdrun didnt work. The same file seems to work properly on simple Fedora linux PC, but not on IBM Power linux. Dont know then what the problem is?? could it be th

Re: [gmx-users] RNA ffgmx.hdb problems

[EMAIL PROTECTED] a écrit : Hello all, as a beginner I try gromacs for the first time. At first my aim is just the energy minimization of a small RNA aptamer. I started to convert my pdb file into a gromacs structure file with pdb2gmx and failed. I obtained this error: Fatal error: Atom H1* in

Re: [gmx-users] RNA ffgmx.hdb problems

Hi, On Thursday, 14. June 2007 13:43, [EMAIL PROTECTED] wrote: > Hello all, > > as a beginner I try gromacs for the first time. At first my aim is just > the energy minimization of a small RNA aptamer. I started to convert my > pdb file into a gromacs structure file with pdb2gmx and failed. I obta

Re: [gmx-users] gromacs on IBM Power 5 Linux Machine: Preprocessor problem

Monika Sharma wrote: I am using Gromacs3.3 version, and I was trying grompp for energy minimization, which is not working. Even the mdrun didnt work. The same file seems to work properly on simple Fedora linux PC, but not on IBM Power linux. Dont know then what the problem is?? Well if grompp

Re: [gmx-users] mdrun -glas

Michal Kolinski wrote: Hi all. Can anyone please explain what the mdrun option –glas stands for. I was trying to find some description in GROMACS manual and mailing list but there isn’t much. Thank you in advance Michal Check Title: Properties of adsorbed water layers and the effect of adso

[gmx-users] mdrun -glas

Hi all. Can anyone please explain what the mdrun option -glas stands for. I was trying to find some description in GROMACS manual and mailing list but there isn't much. Thank you in advance Michal -- Ten list został przeskanowany przez program ArcaMail Silnik (2006-01-25/2007-06-14) This mes

[gmx-users] g_dipoles output

Hi Folks, I struggle with the output of g_dipoles, just to make sure that I understood it right: I select a subpart of my simulation and get the following output: > Average volume over run is 216 > > Dipole moment (Debye) > - > Average = 0.4463 Std. Dev. = 0.5010 Err

[gmx-users] Re: OPLSaa+Lipid.itp question

Hi Oliver, Please keep this on the gromacs mailing list. Please feel free to send me a separate email to notify me that you have made a post and to ask for my reply on that list. My answers here are submitted alongside your text below. Oliver Mirus wrote: Hi Chris, I've followed your short

[gmx-users] Re: HB lifetime in g_hbond

I have a question regarding the calculation of hydrogen bond lifetimes in g_hbond: Line 1094 of gmx_hbond.c v 1.16.2.11 2006/04/02 (which is equivalent to line 1121 of gmx_hbond.c v 1.28 2006/08/30) reads: t = hb->time[i] - hb->time[0] - 0.5*dt; leading to the time series 1, 3, 5,.. that doe

[gmx-users] Energy difference - Gromacs, Autodock

Hello Gromacs users! Let me ask you a questions about comparison of energy values resulted from Autodock ligand-receptor docking and Gromacs MD stimulation. The middle potential energy of ligand-receptor interaction (Gromacs, 1000 psec MD stimulation) is about 65 kcal/mol. This seems to be a

[gmx-users] Re: Warning when using both LJ and Buckingham non-bonded interaction

Hi, David, Then it will be quite slow compared if I used the LJ or Buckingham function, right? Yours Sincerely, WU Yanbin -- Message: 6 Date: Thu, 14 Jun 2007 08:21:36 +0200 From: David van der Spoel <[E

[gmx-users] Re: Warning when using both LJ and Buckingham non-bonded interaction

Hi, David, Then it will be quite slow using potential table compared if I used the LJ or Buckingham function, right? Yours Sincerely, WU Yanbin -- Message: 6 Date: Thu, 14 Jun 2007

Re: [gmx-users] Energy difference - Gromacs, Autodock

Александр Журавлев wrote: Hello Gromacs users! Let me ask you a questions about comparison of energy values resulted from Autodock ligand-receptor docking and Gromacs MD stimulation. The middle potential energy of ligand-receptor interaction (Gromacs, 1000 psec MD stimulation) is about 65 kcal

Re: [gmx-users] Re: Warning when using both LJ and Buckingham non-bonded interaction

WU Yanbin wrote: Hi, David, Then it will be quite slow using potential table compared if I used the LJ or Buckingham function, right? Yours Sincerely, WU Yanbin It is slower than LJ, but not (much) slower

Re: [gmx-users] g_dipoles output

Martin Höfling wrote: Hi Folks, I struggle with the output of g_dipoles, just to make sure that I understood it right: I select a subpart of my simulation and get the following output: Average volume over run is 216 Dipole moment (Debye) - Average = 0.4463 Std. Dev.

[gmx-users] Urea molecule deformed in urea-water simulations using ffamber99

Hi, I am doing a simple simulation of one urea molecule dissolved in water. I am using the ffamber_urea.itp introduced in the AMBER port for GROMACS. I build a box using editconf and solvate the urea molecule using genbox with the fftip3p.itp water model also included with the AMBER port.

Re: [gmx-users] Urea molecule deformed in urea-water simulations using ffamber99

George Abadir wrote: Hi, I am doing a simple simulation of one urea molecule dissolved in water. I am using the ffamber_urea.itp introduced in the AMBER port for GROMACS. I build a box using editconf and solvate the urea molecule using genbox with the fftip3p.itp water model also included

Re: [gmx-users] Urea molecule deformed in urea-water simulations using ffamber99

George Abadir wrote: Hi, I am doing a simple simulation of one urea molecule dissolved in water. I am using the ffamber_urea.itp introduced in the AMBER port for GROMACS. I build a box using editconf and solvate the urea molecule using genbox with the fftip3p.itp water model also included