Re: [gmx-users] Saving trajectories of a particular group within the system

Hi Tsjerk, So the claim in the online manual (under http://www.gromacs.org/documentation/reference_3.3/online/mdp_opt.html#g eneral), that "the difference between a dash and an underscore is ignored", is incorrect according to you? Or is it only incorrect for the option "xtc-groups"? If incorrect

[gmx-users] RE: problem with result from g_rdf

So how large is this "small factor" compared to the rdf values? And does this factor remain exactly constant as a function of r? I'm only guessing, but it could be due to a slight difference in the r used by you and by g_rdf (or equivalently a difference in the location of a bin relative to r). Pe

[gmx-users] Search doesn't work past May 2007

Hi guys, I noticed that at this moment the mailing list search on the GROMACS website only gives results from before some date in May 2007. So it seems to me that the search database hasn't been updated since then. Is this done on purpose or is something wrong? For gmx-users there is a way around

[gmx-users] Dihedral with parameters set to zero

Hi guys, Probably too simple for you guys, but I just need to be sure: Am I right if I say that a GROMOS96 proper dihedral with all parameters set to 0 (done automatically by grompp) is exactly equivalent to no proper dihedral at all, both with respect to all the energy terms and with respect to

Re: [gmx-users] Dihedral with parameters set to zero

w. >Date: Wed, 09 Jan 2008 20:41:19 +0100 >From: David van der Spoel <[EMAIL PROTECTED]> >Subject: Re: [gmx-users] Dihedral with parameters set to zero >To: Discussion list for GROMACS users >Message-ID: <[EMAIL PROTECTED]> >Content-Type: text/plain; charset=ISO-885

[gmx-users] RE: gmx-users Digest, Vol 45, Issue 28

Hi Soni, I have never had such problems, but only some suggestions: 1) Try the PRODRG beta server (http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta) 2) Try drawing your molecule (or part of it) directly with the JME editor, included on the PRODRG website 3) Try using another input file type,

RE: [gmx-users] Generating topology file for a molecule (FNP) not in the gromacs library.

Hi Soni, I have never had such problems, but only some suggestions: 1) Try the PRODRG beta server (http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta) 2) Try drawing your molecule (or part of it) directly with the JME editor, included on the PRODRG website 3) Try using another input file type,

Re: [gmx-users] Dihedral with parameters set to zero

with parameters set to zero >To: Discussion list for GROMACS users >Message-ID: <[EMAIL PROTECTED]> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed > >van Bemmelen wrote: >> OK. Now I'm confused. What did you mean by the second part? >> >>

[gmx-users] N terminus charge groups in ffG53a6

Hi guys, I have a question about the assignment of charge groups at the N-terminus when applying the GROMOS 53a6 force field. But this may also be relevant to other force fields. When I run pdb2gmx (gmx 3.3.1) on a protein (lysozyme 1AKI in this case), it gives the following N terminus topology:

Re: [gmx-users] Rugged dG/dlambda when turning off charges

Hi Bob, Yes, when only turning off charges sc_alpha can be safely set to zero. This will probably give you a much smoother result, although I'm not sure if it will take care of the enormous fluctuations you are seeing. Have you done any error analysis? Maybe you're just experiencing very bad conv

[gmx-users] RE: Patch for PME in Free Energy?

Hi Justin, I can understand that you want your "forward" and "reverse" direction results to be equal for verification reasons. But keep in mind that there really is no "forward" or "reverse" direction when doing TI on separately equilibrated (i.e. independent for every lambda) starting stuctures (

RE: [gmx-users] Strange dgdl-value together with lincs

Maik, This is just a hunch, but since you're turning charges on (instead of off) in the third step, maybe this is also a case of bug 175 (http://bugzilla.gromacs.org/show_bug.cgi?id=175). That is, if you're using PME for electrostatics. This bug has been fixed for the CVS version. Another "fix" w

Re: [gmx-users] Strange dgdl-value together with lincs

Hi Maik, >From: Maik Goette <[EMAIL PROTECTED]> >Subject: Re: [gmx-users] Strange dgdl-value together with lincs > >Jeroen, > >I'm aware of that bug and using the 3.3.2_pre, with the bugfix >included. OK. No problem there then. As I said, it was just a guess. >Btw, I don't see how to sample "ba

RE: [gmx-users] Free energy calculations and speed problems

Hi Justin, You shouldn't use PME in vacuo. Just use pbc=no and infinite (i.o.w.: no) cutoffs. I'm not entirely sure why PME takes such a long time, but I can give a very wild guess. It may have something to do with the fact that, if I remember correctly, the Fourier transform of one (or a few)

[gmx-users] RE: g_mindist option

Hi Alka, >So according to the header information the third column (all >0.00) is the information for maximum internal distance but i >am not getting what it conveys. >From the manual of g_mindist (http://www.gromacs.org/documentation/reference/online/g_mindist.html): "It also plots the maximum

[gmx-users] Article gallery

Hi, Just to let you guys know, the 'article gallery' on the gromacs website doesn't seem to work anymore. mzzls Jeroen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at h

RE: [gmx-users] Timestep

Ramya, A timestep of dt=0.002 already means a timestep of 2fs, since the unit of dt is ps. So a timestep of dt=0.002=2 fs works fine for you, which is perfectly normal. If you want to go higher you need to use certain tricks, as suggested by Xavier. I suggest you read the manual (e.g. http://www.

Re: [gmx-users] pressure scaling more than 1%

Hi Wang Qin, It sounds to me like (part of) your structure immediately starts collapsing during equilibration. So I have a couple of suggestions: 1) It may help to take a look at the trajectory file from those first 500 steps, to see what's really going on physically. 2) Please make sure you al

Re: [gmx-users] how to build up fixed connections? how to simulate no electrostatics?

Hi all, As a side note: although I also have some trouble figuring out what Nicolas Schmidt is exactly trying to do, I find the question "what to do to totally switch the electrostatics off?" to be quite intriguing. It is my understanding that when you simply set rcoulomb=0, this actually means an

Re: [gmx-users] how to build up fixed connections? How to simulate no electrostatics?

p=yes; format=flowed > >Hi Jeroen, > >Just set the charges to zero - then the program will automatically >detect it and use LJ-only loops everywhere. > >Cheers, > >Erik > >On Aug 15, 2007, at 8:12 PM, van Bemmelen wrote: > >> Hi all, >> >> As

[gmx-users] RE: Neutralising charge distribution

Hi George, Yes, such a correction term exists, but it's a divergent term. This term is IMPLICITLY included in the energy, since it compensates for the divergent part in the reciprocal space term, leaving a constant term. This constant term is included explicitly in the code. You could take this c

[gmx-users] RE: Neutralising charge distribution

Hi George, Sorry, I got a bit carried away. Actually, I once thought of somehow taking it out myself, so probably that's why. ;-) About the dipole correction: I haven't experimented with it myself, but I'm pretty sure it's switched off when epsilon_surface is 0. That's also what the manual says (

[gmx-users] RE: Neutralising charge distribution

Actually, I'd say they're not incorrect, but incomplete (well, for many systems). There's no mention of the correction terms George was asking about, only the self correction term is taken into account in those equations. But they're in the code allright, and a lot can be induced from the mdp param

[gmx-users] RE: VDW Default and PME question

It's already in the manual (http://www.gromacs.org/documentation/reference/online/mdp_opt.html#gene ral): "Default values are given in parentheses. The first option is always the default option." Maybe a bit confusingly formulated though for a new user. Jeroen >For enumerated option the default

Re: [gmx-users] getting a good .gro file from a pdb file while the topology is ready

Hi, I've noticed this too and indeed it can be a bit irritating. For example: editconf doesn't recognize the HOH residue when changing the box density (see also http://www.gromacs.org/pipermail/gmx-users/2007-January/025611.html). Of course it's not a big problem, and maybe there's a very good re

Re: [gmx-users] Different nstxout and nstvout in mdp file gives totally different trajectory

Hi Tanping, This may seem irrelevant, but are you using PME? And which version of GROMACS is it? Greetings, Jeroen >Date: Sun, 7 Oct 2007 08:46:04 -0700 (PDT) >From: Tanping Li <[EMAIL PROTECTED]> >Subject: Re: [gmx-users] Different nstxout and nstvout in mdp file > gives totally differ

Re: [gmx-users] Different nstxout and nstvout in mdp file gives totally different trajectory

eroen, > >I am using gromacs-3.2.1, and PME. Is that the problem? > > >Yours >Tanping > > >--- van Bemmelen ><[EMAIL PROTECTED]> wrote: > >> Hi Tanping, >> >> This may seem irrelevant, but are you using PME? And which >version of >> GROMAC

RE: [gmx-users] Tool for visualizing disulphide bonds

Hi Ozge, I'm not sure what you mean by "visualization". But what about using VMD for trajectory visualization and creating a representation that contains only the sulphur atoms forming the disulphide bonds? If that doesn't answer your question, please be more specific. Cheers, Jeroen >Date: Su

RE: [gmx-users] Long range electrostatic potential

As far as I know it can't be done for individual groups. My best guess is that it has something to do with the 'M' in 'PME'. :-) Greetings, Jeroen >Date: Wed, 17 Oct 2007 12:24:58 +0100 >From: "Georgios Patargias" <[EMAIL PROTECTED]> >Subject: [gmx-users] Long range electrostatic potential >To:

[gmx-users] soft-core potential in combination with PME (sorry, again)

Hi all, After reading several posts on this subject on the mailing list, I'm still a bit confused. In http://www.gromacs.org/pipermail/gmx-users/2005- October/017691.html it is more or less suggested that the implementation of the soft-core potential for free energy calculations in combination

RE: [gmx-users] soft-core potential in combination with PME (sorry, again)

> This problem will (probably) always be present, and has > nothing to do with the singularities in the potentials, > but with the fact that one often has awkward free energy > landscapes at intermediate states. > > Berk. > > > >From: "Jeroen van Bemmelen&qu

RE: [gmx-users] soft-core potential in combination with PME

t; is already very soft, but the Coulomb not very soft, > which could lead to instabilities. > But I have never encountered this. > > Berk. > > > >From: "Jeroen van Bemmelen" <[EMAIL PROTECTED]> > >Reply-To: Discussion list for GROMACS users <[EMAIL

Re: [gmx-users] soft-core potential in combination with PME

Hi David and all, Tanks for your elaboration on the subject. I've done a couple of free energy simulations myself, also on disappearing charged atoms, but so far I've not yet encountered any of the instability problems you mention here (though I did encounter instabilities at high lamda values

[gmx-users] error estimates of free energy calculations

Dear GROMACS users, To test my protocol, I have been trying to reproduce some of Berk Hess's hydration free energy results from his 2006 paper (J. Phys. Chem. B 110, 17616-17626, 2006). Although my obtained average free energies are quite comparable, my error estimates are much higher than the

Re: [gmx-users] error estimates of free energy calculations

Hi David and Berk, Thanks a lot for all of your suggestions, which I used to take another look at my protocol. And I think I've found the main source of my problem: Starting with a file containing three columns (for lambda, dG/dl, and the error in dG/dl calculated by "g_analyze -ee"), I ran "g

Re: [gmx-users] free energy tutorial results

Robert, Please check your units: GROMACS uses kJ/mol, while the tutorial uses kcal/mol, if I remember correctly. So there's a factor 4.2 between those two. Jeroen > Date: Thu, 24 May 2007 13:59:58 -0400 > From: "Robert fiske" <[EMAIL PROTECTED]> > Subject: [gmx-users] free energy tutorial res

[gmx-users] website problems

L.S., Just to let you guys know, I'm experiencing some problems with the www.gromacs.org website. E.g.: whenever I press the 'DOCUMENTATION' button on the top menu I get the related page, but not the related submenu on the left side. And whenever I press the 'News' button on the main menu on t

[gmx-users] Regarding polymer equillibration (pressure changes)

Hi Ann, > So my first question is > > wether this can be possible or not? or am I doing something wrong? > if so, then how can i rectify the same error? I think you should definitely use 'editconf -density' to rescale your simulation box to the right density. editconf automatically rescales

[gmx-users] Re: generation of a box of water

Hi Kat, > Thank you for the suggestion. The difficulty is that I want to have a box > with a higher than average density, and gromacs seems to have problems with > this. I have tried the genbox -cs -o water.pdb -boxcommand and > have tried -nmol and -maxsol, but i can't get it to give me a

Re: [gmx-users] freezing/position restraints and minimization

Hmm, interesting... And what about the -DFLEXIBLE definition in your mdp file during steepest descent minimization? Do you know if that will also deform your (SPC) water molecules? And will that deformation be corrected again during the first equilibration step(s)? I ask this, because I read o