[gmx-users] Regd. no PBC
David
spoel at xray.bmc.uu.se
Fri Sep 26 22:25:01 CEST 2003
On Fri, 2003-09-26 at 22:16, Anjan Raghunathan wrote:
> Hi,
> I'd like to know how the No Periodic Boundary Condition switch works. Does it blow up the system over time when dealing with electrostatic systems?Does the box size get updated every time step?Or is there some scheme to maintain the constant box size?
>
it's a vacuum simulation, so your atoms/molecule may evaporate. box is
not used for anything and e.g. pressure is meaningless.
typical options are:
nslist = 0
rcoulomb = 0
rlist = 0
rvdw = 0
this means no cut-off, and make a list only once. Very high performace
simulations, but scaling as N^2.
> thanks
> Anjan
>
>
>
> ---- Original message ----
> >Date: Tue, 26 Aug 2003 12:00:02 +0200
> >From: gmx-users-request at gromacs.org
> >Subject: gmx-users digest, Vol 1 #948 - 5 msgs
> >To: gmx-users at gromacs.org
> >
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> >
> >
> >Today's Topics:
> >
> > 1. Re: growing ligands in binding pockets (Xavier Periole)
> > 2. trjconv (Tanos)
> > 3. Re: trjconv (Xavier Periole)
> > 4. RE: trjconv (Marco Ceruso)
> > 5. Re: GROMACS question (K.A. Feenstra)
> >
> >--__--__--
> >
> >Message: 1
> >From: "Xavier Periole" <periole at inka.mssm.edu>
> >To: <gmx-users at gromacs.org>
> >Subject: Re: [gmx-users] growing ligands in binding pockets
> >Date: Mon, 25 Aug 2003 13:16:47 -0400
> >Reply-To: gmx-users at gromacs.org
> >
> >
> >Hello John,
> >
> >Remember that the apparition/disparition of your ligand is supposed
> >to only be a perturbation to your system. This is a necessary condition
> >for your FEP calculation to be valid. That is why people use a lambda
> >to decompose the "transformation" into perturbations as small as possible
> >within the computer feasability.
> >People have done that for cations alchmistry (good results), or some
> >mutation studies (not sure it works for all kind of mutants), ligand I don't
> >know. I am just trying to stress out the bigger the perturbation the less
> >accurate the result !!
> >
> >
> >XAvier
> >
> >
> >
> >
> >--__--__--
> >
> >Message: 2
> >Date: Mon, 25 Aug 2003 14:20:50 -0300
> >From: Tanos <tccf at epq.ime.eb.br>
> >To: gmx-users at gromacs.org
> >Subject: [gmx-users] trjconv
> >Reply-To: gmx-users at gromacs.org
> >
> > Hi folks,
> > I have finished a MD simulation on a protein in a water box and now I
> >need to eliminate the water molecules from the .gro file in order to
> >perform the conformational analysis of the protein after MD. I am trying
> >to do this using trjconv but I am not having any success. Could someone
> >say me the right order of comands to use to eliminate the water
> >molecules and create a new .gro file having just the coordinates of the
> >the protein after MD ???? The information about this, from the manual,
> >is not clear for me.
> > I am typing "trjconv -f 'filename.gro' -o 'newfilename'.gro" What am I
> >doing wrong ????????
> > Thanks in advance.
> > Tanos Celmar Costa Franca.
> > IME - Rio de Janeiro - Brazil
> >
> >
> >--__--__--
> >
> >Message: 3
> >From: "Xavier Periole" <periole at inka.mssm.edu>
> >To: <gmx-users at gromacs.org>
> >Subject: Re: [gmx-users] trjconv
> >Date: Mon, 25 Aug 2003 13:31:53 -0400
> >Reply-To: gmx-users at gromacs.org
> >
> >
> >
> >You have to create an index with the protein (in the default index):
> >
> >make_ndx -f conf-protein
> >
> >generates index.ndx
> >
> >after that you do
> >
> >trajconv -f traj.xtc -n index.ndx -o traj-prot.xtc
> >
> >the program asks you what you want in the output traj
> >
> >XAvier
> >
> >
> >
> >--__--__--
> >
> >Message: 4
> >From: "Marco Ceruso" <mceruso at physbio.mssm.edu>
> >To: <gmx-users at gromacs.org>
> >Subject: RE: [gmx-users] trjconv
> >Date: Mon, 25 Aug 2003 13:31:59 -0400
> >Reply-To: gmx-users at gromacs.org
> >
> >
> >hi-
> >create an index.ndx file with mkae_ndx
> >then trjconv f traj.xtc -o prot.xtc -n index.ndx
> >this will prompt trjconv to read the index file and ask you which group you
> >want for output "Protein" in your case.
> >this will create prot.xtc a trajectory with the protein only
> >Marco
> >
> >
> >-----Original Message-----
> >From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
> >Behalf Of Tanos
> >Sent: Monday, August 25, 2003 1:21 PM
> >To: gmx-users at gromacs.org
> >Subject: [gmx-users] trjconv
> >
> >
> > Hi folks,
> > I have finished a MD simulation on a protein in a water box and now I
> >need to eliminate the water molecules from the .gro file in order to
> >perform the conformational analysis of the protein after MD. I am trying
> >to do this using trjconv but I am not having any success. Could someone
> >say me the right order of comands to use to eliminate the water
> >molecules and create a new .gro file having just the coordinates of the
> >the protein after MD ???? The information about this, from the manual,
> >is not clear for me.
> > I am typing "trjconv -f 'filename.gro' -o 'newfilename'.gro" What am I
> >doing wrong ????????
> > Thanks in advance.
> > Tanos Celmar Costa Franca.
> > IME - Rio de Janeiro - Brazil
> >
> >_______________________________________________
> >gmx-users mailing list
> >gmx-users at gromacs.org
> >http://www.gromacs.org/mailman/listinfo/gmx-users
> >Please don't post (un)subscribe requests to the list. Use the
> >www interface or send it to gmx-users-request at gromacs.org.
> >
> >
> >
> >--__--__--
> >
> >Message: 5
> >Date: Tue, 26 Aug 2003 10:58:36 +0200
> >From: "K.A. Feenstra" <Feenstra at chem.vu.nl>
> >Organization: Vrije Universiteit Amsterdam - Pharmaceutical Chemistry
> >To: gmx-users at gromacs.org
> >CC: "J.Raul Grigera" <grigera at iflysib.unlp.edu.ar>
> >Subject: [gmx-users] Re: GROMACS question
> >Reply-To: gmx-users at gromacs.org
> >
> >J.Raul Grigera wrote:
> >> Dear Anton,
> >> I am trying to produce a simulation with a 'non -existing'
> >> atoms. When producing the .gro files trough editconf I can not tell
> >> him the van der Waals radius. Using the option -vdwd 2.5 (is a big
> >> atom!) always assign the default value. Can you help me?
> >
> >I'm not sure what you are trying to do. Could you explain in more detail?
> >Furthermore, please direct your question to the Gromacs users mailing list
> >(gmx-users at gromacs.org, subscribe at the website www.gromacs.org).
> >
> >
> >--
> >Groetjes,
> >
> >Anton
> > _____________ _______________________________________________________
> >| | |
> >| _ _ ___,| K. Anton Feenstra |
> >| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
> >|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
> >| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
> >| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
> >| | "If You See Me Getting High, Knock Me Down" |
> >| | (Red Hot Chili Peppers) |
> >|_____________|_______________________________________________________|
> >
> >
> >
> >--__--__--
> >
> >_______________________________________________
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> >
> >End of gmx-users Digest
> _______________________________________
>
> Anjan V. Raghunathan
> Graduate Research Assistant
> Computational Electronics Group
> 3213 Beckman Institute,
> Univ. of Illinois at Urbana-Champaign.
>
> E-mail:araghuna at uiuc.edu
> Off: 217-244-1964
> Res: 217-355-5418
> _______________________________________________
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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