Re: [gmx-users] incomparable results with files produced with gromacs3.2.1 and 3.3.1

Hi Tsjerk and Mark, thanks for the answers. The topologies differ in one atom which is changed from NR in the old topology to N in new topology and also, there is one dihedral angle not defined in the old topology and then zero is used by grompp. In the new topology, the dihedral is defined a

Re: [gmx-users] incomparable results with files produced with gromacs3.2.1 and 3.3.1

Hi, Pedro, thanks for the answer. So far I've done several simulations with a theoretical model of aromatase enzyme and I've always used grompp for the mdrun without the trr from the energy minimisation and the simulations have been succesfull. So, maybe this was not the problem this time but

Re: [gmx-users] incomparable results with files produced with gromacs3.2.1 and 3.3.1

Sampo Karkola wrote: Thanks for the quick answer! I did gmxcheck for the em and md tpr-files and they do differ on lot of things. However, I do not know what these differences mean. I was looking for some documentation about the output from gmxcheck but couldn't find any, so if someone has so

[gmx-users] POPC membrane simulations

If I understand correctly you want to construct popc.itp from the dppc.itp that is available on Tieleman's site? And you have used PRODRG to do this? That sounds like a lot of extra work when popc.itp is directly available from Tieleman's site... http://moose.bio.ucalgary.ca/index.php?page=Stru

[gmx-users] pbc_dx specific compilation or linking problem

I have installed gromacs successfully on many systems. Recently I found that for two installations pbc_dx is not working properly. I initially found that this is the case when using one of my own programs built on template.c. I made that program more verbose and found that there are tens of suc

[gmx-users] Counter ion and PME

Dear Gromacs users, I have read in CSC Course Material that it is possible to do not add counter ions in a charged system with PME electrostatics , because gromacs (3.3.1 ?) adds a background uniform charge to neutralize the system. Is this neutralization correct and used in literature? Thanks for

Re: [gmx-users] incomparable results with files produced with gromacs3.2.1 and 3.3.1

Hi Sampo, Thank you for the elaborate account of your problem :) So, the problems seem not to be due to grompp, since, when you use the old .gro .mdp .top files and run grompp on them, you get the behaviour expected from the simulation. Therefore, something happens before. It would be very helpf

Re: [gmx-users] force field

Hi, This is the kind of stuff OPLS excels at, although you'll have to hack the topology more or less manually. Look at OPLS-AA atom types #465-473 and #490-492. Cheers, Erik On Mar 22, 2007, at 7:50 PM, Ashish Gupta wrote: Hello gromacs users, Can anybody suggest me some reference

[gmx-users] force field

Hello gromacs users, Can anybody suggest me some reference where I can look up force field for simple alkanes and ethoxy, propoxy groups (.i.e. -CH2-CH2-O- and -CH2-CH(CH3)-O- chains). I used the prodrg server (using the gromos87 force field) but I did not get results I expected (I would expe

Re: [gmx-users] incomparable results with files produced with gromacs3.2.1 and 3.3.1

Hi Sampo, I don't know if this is obvious to you but when you start a simulation from a energy-minimized configuration you should use *grompp -t minimization.trr -c minimization_out.gro* (here you will use a full-precision configuration) and not only *grompp -c minimization_out.gro* (in contr

Re: [gmx-users] incomparable results with files produced with gromacs3.2.1 and 3.3.1

Thanks for the quick answer! I did gmxcheck for the em and md tpr-files and they do differ on lot of things. However, I do not know what these differences mean. I was looking for some documentation about the output from gmxcheck but couldn't find any, so if someone has some guides on how to re

Re: [gmx-users] incomparable results with files produced with gromacs3.2.1 and 3.3.1

Sampo Karkola wrote: Dear list, Thanks for the good problem description! I am trying to simulate a crystal structure of a protein with a cofactor (NADP, I've used NDPP topology) and a (self-made) ligand in a box of water. The preparation of the simulation went normally: pdb2gmx, editconf, g

Re: [[gmx-users] genion error!]

Maybe you forgot to delete the waters that were removed in the ionization process? /Pär > Dear users: > I want to prepare protein simulation on 0.15mol/l salt > concentration,I use > genion command to add ions,After genion,I change cln.top file last > line to NA+ > 61,CL- 41. >When I

Re: [gmx-users] information on Na Channels in lipid bilayers ?

Hi Sridhara, One fairly recent paper (about a year old) on the structure of a Na+/K+ conducting channel is: Shi, Ye, Alam, Chen & Jiang, Nature 440 (23):570-4. /Pär On Thu, 2007-03-22 at 12:00 +0100, [EMAIL PROTECTED] wrote: > Message: 1 > Date: Wed, 21 Mar 2007 15:11:15 -0400 > From: "Viswanadh

Re: [gmx-users] mindist during MD

andrea spitaleri wrote: Hi sorry for the poor information. I have used PME with rlist = rcoulomb = rvdw = 0.9 (as I said) and the g_mindist is between the protein-protein system thanks So that number is the distance between the protein and it's periodic image? In that case it is a bit short.

[gmx-users] incomparable results with files produced with gromacs3.2.1 and 3.3.1

Dear list, I am trying to simulate a crystal structure of a protein with a cofactor (NADP, I've used NDPP topology) and a (self-made) ligand in a box of water. The preparation of the simulation went normally: pdb2gmx, editconf, genbox, grompp (for ions), genion, grompp (for em) mdrun (em), gr

Re: [gmx-users] mindist during MD

Hi sorry for the poor information. I have used PME with rlist = rcoulomb = rvdw = 0.9 (as I said) and the g_mindist is between the protein-protein system thanks Regards, andrea David van der Spoel wrote: > [EMAIL PROTECTED] wrote: >> Hi all, >> my rlist = rcoulomb = rvdw = 0.9 and during my si

Re: [gmx-users] turn off pdb output

Hi David, It doesn't matter - we just check if it is set at all, i.e. whether getenv("NO_SHAKE_ERROR") returns NULL or not. Cheers, Erik On Mar 22, 2007, at 12:59 AM, David Mobley wrote: Berk, What value does this need to be set to for it to work? Thanks, David On 3/20/07, Berk Hess