Re: [gmx-users] General Questions about Molecular Dynamics

2011-12-25 Thread Jussi Lehtola
On Sun, 25 Dec 2011 20:45:44 + (GMT) Lara Bunte wrote: > Hello > > I have a few questions about molecular dynamics simulations. > > 1) For a molecule Newton's equation of motion is solved. Do I get > here one resulting force for the hole molecule or do I get a lot of > forces, one for each a

Re: [gmx-users] General Questions about Molecular Dynamics

2011-12-25 Thread Mark Abraham
On 12/26/2011 7:45 AM, Lara Bunte wrote: Hello I have a few questions about molecular dynamics simulations. 1) For a molecule Newton's equation of motion is solved. Do I get here one resulting force for the hole molecule or do I get a lot of forces, one for each atom? 2) The force is calcul

Re: [gmx-users] General Questions about Molecular Dynamics

2011-12-25 Thread Justin A. Lemkul
Lara Bunte wrote: Hello I have a few questions about molecular dynamics simulations. 1) For a molecule Newton's equation of motion is solved. Do I get here one resulting force for the hole molecule or do I get a lot of forces, one for each atom? Forces per atom at each timestep can be w

Re: [gmx-users] Atomtype not found - grompp - charmm27 and charmm22

2011-12-25 Thread Justin A. Lemkul
Lara Bunte wrote: Hi, first thanks for help. I have two questions. 1.) Is this mail going to the mailing list or only to you? If only you get it, how to answer in my thread in the mailig list? The mail went to the mailing list. Respond to the post by sending to gmx-users@gromacs.org.

[gmx-users] General Questions about Molecular Dynamics

2011-12-25 Thread Lara Bunte
Hello I have a few questions about molecular dynamics simulations. 1) For a molecule Newton's equation of motion is solved. Do I get here one resulting force for the hole molecule or do I get a lot of forces, one for each atom? 2) The force is calculated from the potential. This consists of th

Re: [gmx-users] Atomtype not found - grompp - charmm27 and charmm22

2011-12-25 Thread Justin A. Lemkul
Lara Bunte wrote: Hello I took parameters that are calculated for a charmm22 forcefield and I want to use it with a charmm27 forcefield (I have the same molecule as the people who calculated the charmm22 parameters but they didn't use gromacs). I made a .rtp, .hdb and residuetypes.dat fi

[gmx-users] Atomtype not found - grompp - charmm27 and charmm22

2011-12-25 Thread Lara Bunte
Hello I took parameters that are calculated for  a charmm22 forcefield and I want to use it with a charmm27 forcefield (I have the same molecule as the people who calculated the charmm22 parameters but they didn't use gromacs).  I made a .rtp,  .hdb and residuetypes.dat file and edit the atomty

Re: [gmx-users] Gravity or weightlessness condition

2011-12-25 Thread David van der Spoel
On 2011-12-25 14:30, Shahrbanoo Karbalaee wrote: Dear I want to simulate cell membranes in weightlessness condition ( the same as space).Would you please tell me Can I run with Gromacs? If Yes with which parameters? Best It is weightless by default! Isn't that great? But seriously for most m

[gmx-users] Gravity or weightlessness condition

2011-12-25 Thread Shahrbanoo Karbalaee
Dear I want to simulate cell membranes in weightlessness condition ( the same as space).Would you please tell me Can I run with Gromacs? If Yes with which parameters? Best -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the arc

[gmx-users] how to use gromacs 4.5.5's temple?

2011-12-25 Thread 杜波
Dear teacher, how to use gromacs 4.5.5's temple? i make the temple successful! And when i run it (./template -f traj.xtc -s water.tpr -cutoff 2), the output like this: " Reading file water.tpr, VERSION 4.5.5 (single precision) Reading file water.tpr, VERSION 4.5.5 (single precision) Specify a r

[gmx-users] Announcing the GROMACS Molecule & Liquid Database

2011-12-25 Thread David van der Spoel
Dear all, with great pleasure I am announcing the GROMACS Molecule & Liquid Database at http://virtualchemistry.org. The website holds *validated* itp files and liquid structures for 146 molecular liquids. For all liquids eight different simulated properties and (where available) experimenta

Re: [gmx-users] Fw: modifying the mutated DNA parameters

2011-12-25 Thread banafsheh mehrazma
Dear all;   As you all  know, in all of the force fields in Gromacs package, G,C,A and T are known. In your opinion, what should I do in case of 8-OxoG?  How to obtain parameters needed for this new residue?   Thank you   B.Mehrazma From: Mark Abraham To: Discu

Re: [gmx-users] Temperature de-coupling in Langevin Dynamics

2011-12-25 Thread David van der Spoel
Op 25 dec 2011 om 09:21 heeft Inon Sharony het volgende geschreven: > Good morning, Mark! > > How do I officially request this as a feature of the next version of GROMACS? > Post to the developers' forum? > Your best bet is to implement it yourself and test it and send a proposed patch to

[gmx-users] oligosaccharide oplsaa .itp

2011-12-25 Thread Ashalatha Sreshty
Dear All, I have a problem running gromacs for a oligosaccharide. it has 14 units sugars containing glucose, mannose and N-acetyl glucosamine units. I want to do MD simulations for this with opls aa force field. For this I have generated the .itp files using topolgen (edited the atoms according to

Re: [gmx-users] Temperature de-coupling in Langevin Dynamics

2011-12-25 Thread Inon Sharony
Good morning, Mark! How do I officially request this as a feature of the next version of GROMACS? Post to the developers' forum? Thanks, Inon. On Saturday, December 24, 2011 12:24:11 PM UTC+2, Mark Abraham wrote: > > On 12/24/2011 6:23 PM, Inon Sharony wrote: > > Good morning! > > I'm runnin