Re: [gmx-users] --enable-threads fails.

Hi, The prefetching hardware is pretty good at hiding latencies, but obviously you'll get better performance when everything fits in cache. However, the largest data structures by far are the neighborlists, and their _total_ size for the simulation is independent of whether you are using

Re: [gmx-users] BHIS for HIS?

Hi, pdb2gmx tries to choose the HIS protonation based on hydrogen bond patterns in the structure, so unless you are absolutely certain you need the alternative state you should need to do anything. In the latter case, just edit the name in the PDB file (to HISB or HISH) prior to running

Re: [gmx-users] total simulation time for proteins in general

Hi, On Apr 11, 2007, at 7:26 AM, Priya Chandran wrote: 2. Is minimisation in GROMACS only used as a precursor to the md- simulation to remove bad contacts, or can we also use it effectively to minimize a raw modelled ab-initio structure.? Well, technically you can of course use it, but

[gmx-users] question about the total-energy of energy minimization

Hi all, I run an energy minization, then calculated the energy, obtained the following results: LJ-(SR)-4431.621905.29 1886.7 -27.08 - 919.923 Coulomb-(SR) -35926.514398.414389.9 -50.5129 -1715.95 Potential -46818.1

[gmx-users] energy minimization error

hello,everyone I am new of gromacs. I am running a sample following the Tutorial for Drug - Enzyme Complex,which was written by John E.Kerrigan,Ph.D. When I run the energy minimization ,it has error as followed. Range checking error: Explanation: During neighborsearching, we assign each

Re: [gmx-users] energy minimization error

Check your trajectory to visually check whether it has exploded. This may lead you to check all your input files, especially the mdp files. This error may happen even in good settings, but Variable ci shall not differ much from the desired range. In that case, I will turn Pressure coupling off

[gmx-users] overcome the integration problem (installing CVS)

Shalom all, To my best understanding, there is a correction to the single precision integration problem (A common, avoidable source of error in molecular dynamics integrators J. Chem. Phys. 126, 046101 (2007).) at the CVS. I want to know were can I get it and how to install it. First, the

Re: [gmx-users] overcome the integration problem (installing CVS)

On 4/11/2007 5:52 PM, Dr Itamar Kass wrote: Shalom all, To my best understanding, there is a correction to the single precision integration problem (A common, avoidable source of error in molecular dynamics integrators J. Chem. Phys. 126, 046101 (2007).) at the CVS. I want to know were can I

Re: [gmx-users] overcome the integration problem (installing CVS)

Yang Ye wrote: On 4/11/2007 5:52 PM, Dr Itamar Kass wrote: Shalom all, To my best understanding, there is a correction to the single precision integration problem (A common, avoidable source of error in molecular dynamics integrators J. Chem. Phys. 126, 046101 (2007).) at the CVS. I want to

Re: [gmx-users] question about the total-energy of energy minimization

Qiao Baofu wrote: Hi all, I run an energy minization, then calculated the energy, obtained the following results: LJ-(SR)-4431.621905.29 1886.7 -27.08 -919.923 Coulomb-(SR) - 35926.514398.414389.9 -50.5129 -1715.95 Potential

[gmx-users] Hi all

Hi I am new to Gromacs. I would like to simulate oligoether branched polysiloxanes in gromacs. I have the force field availble for the same Whether gromacs will support force filed for polymers containing hetreo atmos like silicon? If so how can I incoroprate this into gromacs? and also How to

Re: [gmx-users] overcome the integration problem (installing CVS)

From: David van der Spoel [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] overcome the integration problem (installing CVS) Date: Wed, 11 Apr 2007 12:13:13 +0200 Yang Ye

Re: [gmx-users] Hi all

ann rose wrote: Hi I am new to Gromacs. I would like to simulate oligoether branched polysiloxanes in gromacs. I have the force field availble for the same Whether gromacs will support force filed for polymers containing hetreo atmos like silicon? Yes - this information is part of the force

[gmx-users] Prot_prep_problem

Hello gromacs users, I am facing a particular problem in the preparation of my protein.I have a NMR derived structure with hydrogens. To prepare my protein i thought of a two step procedure 1)stripping the protein of the hydrogens using -ignh and saving pdb output 2)submitting the pdb output

Re: [gmx-users] Prot_prep_problem

HI Pkmukher, I use to use opls for nmr structures in order to keep the all-hydrogen in the protein and ligand too. However if you want to be sticked with gromos ff I do as follow: 1. prepare my system with -ignh option in pdb2gmx 2. run the simulation 3. use protonate over the pdb and the final

Re: [gmx-users] Prot_prep_problem

I apology for the incorrect spelling of your name ... I have an automatic reply format which sometimes does weird stuff ... Sorry Prasenjit, really. Regards andrea andrea spitaleri wrote: HI Pkmukher, I use to use opls for nmr structures in order to keep the all-hydrogen in the protein and

[gmx-users] Prot_prep_query

in advance ann -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20070411/05362ed7/attachment-0001.html -- Message: 5 Date: Wed, 11 Apr 2007 13:40:50 +0200 From: Berk Hess

Re: [gmx-users] overcome the integration problem (installing CVS)

Hi, all- I would like to add that for a constant temperature ensemble the effect of this fix is neglegible. It is only useful for constant NVE simulations. Berk. I think this might need some qualifications. If the constant temperature dynamics are based inherently on NVE dynamics, they must

Re: [gmx-users] overcome the integration problem (installing CVS)

Michael Shirts wrote: Hi, all- I would like to add that for a constant temperature ensemble the effect of this fix is neglegible. It is only useful for constant NVE simulations. Berk. I think this might need some qualifications. If the constant temperature dynamics are based inherently on

[gmx-users] Re:overcome the integration problem (installing CVS)

How about total energy? In tends to be constant in NVE simulations. I don't know what the conserved property would be in an NVT simulation. David. For most algorithms that give correct ensembles, there are pseudo-energy properties that are conserved. For NVE, it's obviously the energy. For

[gmx-users] wall_atomtype

Greetings to All I have a question about a new feature in the cvs code and I was wondering if there was anybody who could give me a hand of a bit of help. Thanks in advanced. I am working on a project that involves simulation of confined water between two hydrophobic surfaces. I noticed that

[gmx-users] Prot_prep_query

Hi, Thanks for your suggestions. I was using the 0 option gromos FF in pdb2gmx. As you said the behavior is strange. However i found a fix. I was using a 2 step procedure 1) strip hydrogen output pdb 2) input pdb write output pdb with -inter flag instead i used 1) strip hydrogen output