Re: [gmx-users] OPLS modification between 3.3 and 3.3.1??

Hi Chris, This change was committed before we had started bugzilla, so thus no entry, but you can find it in the CVS log :-) It was covered on the mailing list, though. The torsion only affects non-standard protonation states of side chains that are not present in any OPLS-AA publication.

Re: [gmx-users] Unnatural amino acid problems

> Hello > I am parametrizing an unnatural amino acid, phenylglycine (PHG), in > the OPLS FF in GROMACS. I have put in the necessary parameters in > the .hdb, .rtp, and the aminoacids.dat file. > 1. When I do grompp for the EM, I get an error saying that I have not > put in the appropriate parameter

Re: [gmx-users] OPLS modification between 3.3 and 3.3.1??

[EMAIL PROTECTED] wrote: Hello, ffoplsaa.rtp has changed in the 3.3.1 release. However, there are no references given and no special notification of this fact. I was wondering if anybody knows the references for this change. Searching for opls_210 or dih_LYSH_chi5_C_C_N_H on the mailing lists

[gmx-users] Unnatural amino acid problems

Hello I am parametrizing an unnatural amino acid, phenylglycine (PHG), in the OPLS FF in GROMACS. I have put in the necessary parameters in the .hdb, .rtp, and the aminoacids.dat file. 1. When I do grompp for the EM, I get an error saying that I have not put in the appropriate parameters for

Re: [gmx-users] Installation Error on an Athlon64 with Intel Compiler

Jones de Andrade wrote: Hi all! I'm trying to compile gromacs 3.3.1 on an Athlon64 (core venice) with the intel compiler (icc version 9.0.030). I've tried a lot of flags, and also no flags. All times I get the following error, after which everything fails: It is not related to FLAGS. /usr/lo

[gmx-users] Doubt in Distance Restraints

Dear all, My intention is to restrict Fe(II) in active site by distance restraint protocol. Fe(II) is ligated by three amino acides' polar atoms respectively by (1) NE2 of HIS ,(2) NE2 of HIS (3) OD1 of ASP. The following is the disres itp file I used (copied from manu

[gmx-users] Installation Error on an Athlon64 with Intel Compiler

Hi all! I'm trying to compile gromacs 3.3.1 on an Athlon64 (core venice) with the intel compiler (icc version 9.0.030). I've tried a lot of flags, and also no flags. All times I get the following error, after which everything fails: . . . /usr/local/intel/bin/icc -DHAVE_CONFIG_H -I. -I. -I../../.

[gmx-users] LINCS Warning with MDRUN - Segmentation Fault

HiAttached is part of the gro file which gave the LINCS error on atoms. Thisoutput is the gro file for the initial mdrun, after which final grompp andfinal mdrun was done, which gives the error I described in the message below.Gaurav Gaurav Chopra wrote:> > Hi> >> > I am getting the following error

[gmx-users] Please Help: Still facing problems with installing Gromacs 3.3.1 on SGI Irix

SUBJECT: Still facing problems with installing Gromacs 3.3.1 on SGI Irix   Hi   As suggested by Dr. Spoel, I removed one of the semicolons before the double semicolon in one of the lines in the file gmx_chi.c   I re-installed again and this time it gave me the following error. Can you

[gmx-users] OPLS modification between 3.3 and 3.3.1??

Hello, ffoplsaa.rtp has changed in the 3.3.1 release. However, there are no references given and no special notification of this fact. I was wondering if anybody knows the references for this change. Here is the difference between the two distributions: diff ~/TEST/gromacs-3.3/share/top/ffoplsa

Re: [gmx-users] FFTW installation error: cannot compile a simpleFortran program

hi, simple install first fftw with: grep fftw from fftw site wget http://www.fftw.org/fftw-3.1.1.tar.gz unpack ./configure --prefix=/hereyourdirectorywhereyoucanwrite make && make install than do: setenv LDFLAGS -L/raid1/haberl/bin/fftw/3.0.1-32/lib setenv CPPFLAGS -I/raid1/haberl/bin/fftw/3.

[gmx-users] g_sdf for Gromacs 3.3 or any other tool for Spatial Distributions .

Dear all, Does anybody have the g_sdf ported for GROMACS 3.3 ? The g_sdf is a program for calculations of Spatial Distribution Functions (SDFs). It is not from the official distribution - it is written by Christoph Freudenberger whom I am not able to find (his old e-mail is expired). I've got

Re: [gmx-users] Drug Enzyme Tutorial - mdrun segmentation fault

This is probably the result of a bug in 3.3, fixed in 3.3.1. Setting pme_order = 4 is a workaround in case you don't want to upgrade to 3.3.1. --Tom On Apr 19, 2006, at 11:05 AM, Zorzan Simone wrote: Hi all, I am trying to do the Drug Enzyme tutorial (trp_drug_tutor.pdf), on a linux box

RE: [gmx-users] GROMACS 3.3.1 installation on SGI (Irix): 3

Hi ALL I got a lot of errors when I did the modifications in the file make_edi.c in the mnt1.usr/akshayp/src/tools/ Around 101 errors in the same file I do not understand why all these errors are happening. Please help me to take care of these errors and install GROMACS 3.3.1 on SGI Irix. Look

Re: [gmx-users] Huge fluctuations for pressure coupling

Bob Johnson wrote: Hello everyone, I have a 20 base single stranded DNA with counterions that is hydrated with about 9000 water molecules. My pressure coupling input looks like this: pcoupl = Parrinello-Rahman pcoupltype = isotropic ref_p = 1.01 compressibi

[gmx-users] Huge fluctuations for pressure coupling

Hello everyone, I have a 20 base single stranded DNA with counterions that is hydrated with about 9000 water molecules. My pressure coupling input looks like this: pcoupl = Parrinello-Rahman pcoupltype = isotropic ref_p = 1.01 compressibility = 4.5e-5 ta

[gmx-users] Drug Enzyme Tutorial - mdrun segmentation fault

Hi all, I am trying to do the Drug Enzyme tutorial (trp_drug_tutor.pdf), on a linux box (suse 10.0) and Gromacs 3.3. Everything is fine until this command: nohup mdrun -s trp_pr.tpr -o trp_pr.trr -c trp_b4md.gro -g pr.log -e pr.edr That ends abnormally with a segmentation fault. I searched the m

Re: [gmx-users] trjcat -settime option

Thank you so much, Yang Ye. Masa From: Yang Ye <[EMAIL PROTECTED]> Subject: Re: [gmx-users] trjcat -settime option Date: Wed, 19 Apr 2006 21:00:59 +0800 > I missed this for last mail. The use of gmxcheck is to determine the > "welding" point. So trjconv -b {start_time} -e {end_time} could be

Re: [gmx-users] FFTW installation error: cannot compile a simple Fortran program

Ge Sunny wrote: To Florian Haberl: I've also tried installing from fftw-3.0.1.tar.gz. Running ./configure can find g77, but another error appears as config.status: error: cannot find input file: rdft/codelets/hc2r/Makefile.in Sounds like a job for the fftw mailing list. To Mark: I use t

Re: [gmx-users] FFTW installation error: cannot compile a simpleFortran program

From: "Ge Sunny" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: Re: [gmx-users] FFTW installation error: cannot compile a simpleFortran program Date: Wed, 19 Apr 2006 13:32:14 + To Mark: I use the binary fftw3-3.0.1-4 on FC4 with no com

[gmx-users] Re: LINCS Warning with MDRUN - Segmentation Fault (Gaurav Chopra)

Hi Attached is part of the gro file which gave the LINCS error on atoms. This output is the gro file for the initial mdrun, after which final grompp and final mdrun was done, which gives the error I described in the message below. Gaurav Gaurav Chopra wrote:> Hi>> I am getting the following er

Re: [gmx-users] FFTW installation error: cannot compile a simple Fortran program

To Florian Haberl: I've also tried installing from fftw-3.0.1.tar.gz. Running ./configure can find g77, but another error appears as rdft/codelets/hc2r/Makefile.in not found: checking for g77... g77 checking whether we are using the GNU Fortran 77 compiler... yes checking whether g77 accepts

Re: [gmx-users] Paralellization limit?

Andrea Carotti wrote: Hi Carsten, thanks for your quick reply. Could you plese confrim me that gromacs 3.3.1 works and compile fine with mpich 2.x? Yes, compiles and runs in parallel. Only difference is that I use the FFTW3. Carsten Cause this is the first time that I hear that from a user a

Re: [gmx-users] FFTW installation error: cannot compile a simple Fortran program

Florian Haberl wrote: hi On Wednesday 19 April 2006 13:16, Ge Sunny wrote: Hi, I am trying to install FFTW from fftw3-3.0.1-4.src.rpm on Fedora Core 4: I use the binary fftw3-3.0.1-4 on FC4 with no complaints. Why not use it? Your system don`t have any working fortran compiler, reinstall

Re: [gmx-users] Paralellization limit?

Hi Carsten, thanks for your quick reply. Could you plese confrim me that gromacs 3.3.1 works and compile fine with mpich 2.x? Cause this is the first time that I hear that from a user and I'll go ahead on this way instead of usin LAM. Thanks again Andrea - Original Message - From: "Car

Re: [gmx-users] Paralellization limit?

Hi Andrea, Andrea Carotti wrote: Hi all, I'm trying to simulate a system with two identical proteins (42aa each one), solvent spc (18430 mols) and 6 ions NA+...for a total of ~56100 atoms. Now the "problem" is that if I run the MD on 4 nodes everything works fine, but when I try to use 6 or

Re: [gmx-users] FFTW installation error: cannot compile a simple Fortran program

hi On Wednesday 19 April 2006 13:16, Ge Sunny wrote: > Hi, > > I am trying to install FFTW from fftw3-3.0.1-4.src.rpm on Fedora Core 4: > > $ rpmbuild --rebuild fftw3-3.0.1-4.src.rpm > > GNU Fortran 3.2.3 g77 is available in the system. However, the installation > fails with the error in Fortran co

[gmx-users] Paralellization limit?

Hi all, I'm trying to simulate a system with two identical proteins (42aa each one), solvent spc (18430 mols) and 6 ions NA+...for a total of ~56100 atoms. Now the "problem" is that if I run the MD on 4 nodes everything works fine, but when I try to use 6 or 8 cpus the process stops on the mast

[gmx-users] FFTW installation error: cannot compile a simple Fortran program

Hi, I am trying to install FFTW from fftw3-3.0.1-4.src.rpm on Fedora Core 4: $ rpmbuild --rebuild fftw3-3.0.1-4.src.rpm GNU Fortran 3.2.3 g77 is available in the system. However, the installation fails with the error in Fortran compilation: ... ... checking for g77... g77 checking whether we

Re: [gmx-users] trjcat -settime option

Thanks for quick reply, Yang Ye and David, But my way of asking seemed not good. I know what trjcat command is. It is to concatinate two .trr files. but when we use trjcat command with -settime option, the command says as following, > c (continue) - The start time is taken from the end > of the

[gmx-users] pdb2gmx error

Hello, gmx-users， i used command"pdb2gmx -f a.pdb -ignh" but i got error like: Program pdb2gmx, VERSION 3.3 Source code file: add_par.c, line: 218 Fatal error: Atom H2 not found in rtp database in residue BEN --- there are no H2

Re: [gmx-users] HOWTO for installing non-MPI gromacs-3.3.1 on cygwin

Hi Mark, Thanks! However, if you drop me a line with the exact names of the FFTW3 libraries/objects you were talking about I'll see if I can fix the autodetection script. Cheers, ERik On Apr 19, 2006, at 4:26 AM, Mark Abraham wrote: Hi, I recently re-installed gromacs 3.3.1 on a Windo