RE: [gmx-users] Unexplained crashes with Gromacs-4.0

Hi, I have no clue what the problem could be. But now I thought a bit longer, I realized that with domain decomposition the ci error should never occur, since the domain decomposition puts the charge groups inside the DD cells, so also inside the ns cells. This seems to indicate that there is a

Re: [gmx-users] Unexplained crashes with Gromacs-4.0

Hi, I think I had a similar error in GROMACS 3.3.1 (I posted it in June to the User List http://www.gromacs.org/pipermail/gmx-users/2008-June/034411.html). I also got a not reproducable error for the ci variable. I made some test and found out that for my system the error occures with

[gmx-users] Problem building a new polymer using pdb2gmx....

Dear users I'm trying to build a polymer with a new building block. I have included the new topology block inside the force field rtp file, which I've choosen for my simulation (ffG53a6.rtp). I've also prepared a gro input file, where the atoms of each residue follows the same order as in

Re: [gmx-users] Problem building a new polymer using pdb2gmx....

Alberto Sergio Garay ha scritto: Dear users I'm trying to build a polymer with a new building block. I have included the new topology block inside the force field rtp file, which I've choosen for my simulation (ffG53a6.rtp). I've also prepared a gro input file, where the atoms of each residue

RE: [gmx-users] Unexplained crashes with Gromacs-4.0

Hi, That issue in 3.3.1 is completely unrelated to this issue in 4.0. Was your problem in 3.3.1 with parrinello-rahman coupling? If so, that problem is probably solved by a bug fix in the PR pressure coupling I introduced in the 4.0 release. Berk Date: Thu, 16 Oct 2008 14:06:19 +0200 From:

[gmx-users] Topology file for fullerene c60

Dear users! I'm trying to make forcefield oplsaa for fullerene. I already have modified files (see it in the end of the letter), but i have a problem with torsion parameters - torsion angles are different, but atom type is the same - alkene. Length and angles were taken as an average. After

Re: [gmx-users] transfer pdb to gro

He, Yang wrote: Hi Justin. I just followed the pdb file from you but I can still not create the correct gro.file. I use this command editconf -f hao.pdb -o hao.gro -d 1.0 What is the problem . And I find what you create for the pdb file based on mine almost makes no difference . I

Re: [gmx-users] transfer pdb to gro

He, Yang wrote: the operating system is unix and the version is about 3.1.1. I have no idea whether this will influence the result. Version 3.1.1 is very old; upgrade to a newer version and try again. -Justin It always shows like this: Opening library file

Re: [gmx-users] transfer pdb to gro

He, Yang wrote: Thank you for your suggestion. I just have a doubt about the pdb file . If we need to carry on some practical problems with the gromacs, how can we get the pdb.fill .Just from the online and then make some modification based on the practical project or just write it by

[gmx-users] GROMACS on Bluegene

Hi, I can see GROMACS 4.0 has inner loops apparently optimized for BlueGene, however the distribution is incomplete. At least the files interaction.h nb_kernel_w3_bluegene.h nb_kernel_w3w3_bluegene.h nb_kernel_w4_bluegene.h nb_kernel_w4w4_bluegene.h nb_kernel_gen_bluegene.h are missing from