Re: [gmx-users] mdp-settings for charmm36 and lipid apl values

of course), and that the results depend to some extent also on the usage of TIP3P vs TIP3SP water models. I have been using "normal" TIP3P here. Could anyone comment on (a) my mdp-file settings, and (b) the resulting APL, and tell me if I should be worried about anything? THANKS -- _

Re: [gmx-users] What is the autocorrelation time

ogy, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 er...@xray.bmc.uu.se <mailto:er...@xray.bmc.uu.se> http://www2.icm.uu.se/molbio/elflab/index.html -- _______

Re: [gmx-users] What is the autocorrelation time

you, Chris. -- original message -- Probably these links give you simple and clear response for your question http://idlastro.gsfc.nasa.gov/idl_html_help/Time-Series_Analysis.html and http://www.statsoft.com/textbook/time-series-analysis/ HTH Stephane -- ______

Re: [gmx-users] a question about ensemble

/j.cpc.2008.01.006. Ciao, Patrick -- _______ Patrick FUCHS Dynamique des Structures et Interactions des Macromolécules Biologiques INTS, INSERM UMR-S665, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-43-06-50-19 E-mai

Re: [gmx-users] a question about ensemble

canonical ensemble (in the old versions of GROMACS it was the only way to get the canonical ensemble before the implementation of Nose-Hoover or velocity rescaling). Ciao, Patrick -- _______ Patrick FUCHS Dynamique des Str

Re: [gmx-users] REST simulation

opology files? Ciao, Otto On Tue, Dec 13, 2011 at 1:23 PM, Patrick Fuchs mailto:patrick.fu...@univ-paris-diderot.fr>> wrote: Hi Otto, you have to equilibrate at each lambda value! The unscaled Hamiltionian is your lowest "temperature", say 300K, which corresponds t

Re: [gmx-users] REST simulation

ifferent replica for different lambda values to interpolate between the two configuration. I would be very glad if you could help me on that. All the best Otto On Mon, Dec 12, 2011 at 1:50 PM, Patrick Fuchs mailto:patrick.fu...@univ-paris-diderot.fr>> wrote: Hi Otto, yes I

Re: [gmx-users] REST simulation

Hi Mark, good to know, this -pp option of grompp is very useful. Thanks! Ciao, Patrick Le 12/12/2011 12:55, Mark Abraham a écrit : On 12/12/2011 8:42 PM, Patrick Fuchs wrote: Hi Otto, in my lab we tried to implement this REST variant in GROMACS as proposed by those authors. We figured out

Re: [gmx-users] REST simulation

go for each replicate through the usual simulation preparation steps (minimisation, nvt, equilibration ...). The result of this you use for the replicate exchange simulation. Thanks a lot Otto On 12 Dec 2011, at 10:42, Patrick Fuchs wrote: Hi Otto, in my lab we tried to implement this REST var

Re: [gmx-users] REST simulation

help. All the best Otto -- ___________ Patrick FUCHS Dynamique des Structures et Interactions des Macromolécules Biologiques INTS, INSERM UMR-S665, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-

Re: [gmx-users] Gromos parameters for atom type OA

, Murcia (SPAIN) T: (0034)868887434 -- _______ Patrick FUCHS Dynamique des Structures et Interactions des Macromolécules Biologiques INTS, INSERM UMR-S665, Université Paris Diderot, 6 rue Alexandre Cabanel, 75015 Paris Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-43-06-50-19 E-mail address: patrick.f

Re: [gmx-users] compressing a box of water droplets into a homogeneous solution of liquid water

pectations/experience of collapse from the gas state to the liquid state under standard NPT conditions? Thank you, Chris. -- ___ new E-mail address: patrick.fu...@univ-paris-diderot.fr !!!! Patrick FUCHS Dynamique des Str

Re: [gmx-users] compressing a box of water droplets into a homogeneous solution of liquid water

ns? Thank you, Chris. -- ___ new E-mail address: patrick.fu...@univ-paris-diderot.fr !!!! Patrick FUCHS Dynamique des Structures et Interactions des Macromolécules Biologiques INTS, INSERM UMR-S665, Université Paris Dide

Re: [gmx-users] Can g_wham support using different temperature for different windows?

- > > *From:* Justin A. Lemkul mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> > > *To:* Gromacs Users' List mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>> &g

Re: [gmx-users] InflateGRO and trimer simulation

error, if it even works, given the very specific nature of what you need. -Justin -- ___ new E-mail address: patrick.fu...@univ-paris-diderot.fr Patrick FUCHS Dynamique des Structures et Interactions des Macromolécule

Re: [gmx-users] problem with 53a6 simulating a coiled-coil fiber like protein

the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ new E-mail address: patrick.fu...@univ-paris-diderot.fr P

Re: [gmx-users] UA simulation of PEO melt

erface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ new E-mail address: patrick.fu...@univ-paris-diderot.fr Patrick FUCHS Dynamique des Struc

Re: [gmx-users] P-N vector orientation

code to calculate the PN vector (using [xN-xP,yN-yP,zN-zP]). Ciao, Patrick Nicolas a écrit : Hello, I just remember that you might be interested by g_tilt developed by Patrick Fuchs.: http://www.dsimb.inserm.fr/~fuchs/download/ <http://www.dsimb.inserm.fr/%7Efuchs/download/> I

Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug?

1.41.3-2.fc10.x86_64 glibc-2.9-3.x86_64 > > > libICE-1.0.4-4.fc10.x86_64 libSM-1.1.0-2.fc10.x86_64 > > > libX11-1.1.4-6.fc10.x86_64 libXau-1.0.4-1.fc10.x86_64 > > > libXdmcp-1.0.2-6.fc10.x86_64 libxcb-1.1.91-5.fc10.x86_64 > > > (gdb) where > > > #0 0x

Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug?

Express yourself instantly with MSN Messenger! MSN Messenger <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> ___ gmx-users mailing li

Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug?

em with gromacs 3.3 and > > gromacs 4 is > > > > > that gromacs 4 is running under suse 11 while gromacs 3.3 is > > running on > > > > > a node with suse 10. But I dont think this can be the problem? > > > > > > > > > > cheers > > > > > Bernhard > > > > > > > > > > > &

Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug?

www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- _ new E-mail address: patrick.fu...@univ-paris-diderot.fr new postal address !!!

Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug?

gt; > > > 3.82346e+05 -2.48883e+06 -3.51313e+05 -2.39119e+06 > > 4.57648e+05 > > > > > > > > > Total Energy Temperature Pressure (bar) Cons. rmsd () > > > > > > > > > -1.93355e+06 3.10014e+02 1.09267e-01 2.14030e-05 > > > > > > > > > > > > > > > > > > DD step 88999 load i

Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug?

03 2.42628e+03 1.20942e+03 5.12341e+04 > > > > > > > LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En. > > > > > > > 3.81539e+05 -2.48602e+06 -3.51307e+05 -2.38929e+06 4.56901e+05 > > > > > > > Total Energy Temperature Pressure (ba

Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug?

> > running on > > > > > a node with suse 10. But I dont think this can be the problem? > > > > > > > > > > cheers > > > > > Bernhard > > > > > > > > > > > > > > > ___ > > >

Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug?

gmx-users-requ...@gromacs.org. > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > -------- > > Express yourself instantly with MSN Messenger! MSN Messenger > > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> > >

Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug?

romacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gro

Re: [gmx-users] flexible organic solvents

he www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- _ new E-mail address: [EMAIL PROTECTED] !!!! new postal address !!! Patrick FUCHS Equipe de Bio

Re: [gmx-users] Problem with lipid simulations

ers Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- _____

Re: [gmx-users] Gromacs force field discussion

www.gromacs.org/mailing_lists/users.php -- _ new E-mail address: [EMAIL PROTECTED] Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fa

Re: [gmx-users] g_dist producing inconsistent values

(un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U

Re: [gmx-users] About g_msd (and noise)

send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75

Re: [gmx-users] About g_msd

D] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1

Re: [gmx-users] Re: Where is the GROMOS87 force field when using pdb2gmx

OTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___________ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANC

Re: [gmx-users] what is the force function for proper dihedrals

subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- _______ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Univer

Re: [gmx-users] Installation/compilation problem ---v3.3.1

list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___________ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Cas

Re: [gmx-users] g_bundle!

subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U72

Re: [gmx-users] Polarizability

only by the fact that the VdW interation is also "floating aroung" in the "shell model" but not in the "charge on a spring" one? Thanks a lot, Jones On 5/21/07, *Patrick Fuchs* <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> wrote: Hi, there&#x

Re: [gmx-users] Polarizability

g/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ Patrick FUCHS Equipe de Bi

Re: [gmx-users] Very large fluctuations in dg/dl

df Best of luck! - John -- John Chodera <[EMAIL PROTECTED]> | Mobile: 415 867-7384 Postdoctoral researcher, Pande lab| Lab phone : 650.723.1097 Department of Chemistry, Stanford University | Lab fax : 650.724.4021 http://www.dillgroup.ucsf.edu/~jchodera On May 8, 2007, at 3.

Re: [gmx-users] Very large fluctuations in dg/dl

operties I'm interested in. Ciao, Patrick Stéphane Téletchéa a écrit : Patrick Fuchs a écrit : Hi Gromacs users, I have a few questions related to solvation free energy calculation via thermodynamic integration. #ifdef FLEX_SPC #include "flexspc.itp" #else #include "sp

Re: [gmx-users] Very large fluctuations in dg/dl

Or didn't you read or understand my previous answer? Reaction-field and PME give exactly the same solvation free-energies, so you can just as well derive parameters for the GROMOS force-field using PME. Berk. From: Patrick Fuchs <[EMAIL PROTECTED]> Reply-To: Discussion list

Re: [gmx-users] Very large fluctuations in dg/dl

f Amino Acid Analogues: A Systematic Comparison of Biomolecular Force Fields and Water Models J. Phys. Chem. B 110, 17616 (2006) http://dx.doi.org/10.1021/jp0641029 Berk. On 5/7/07, Berk Hess <[EMAIL PROTECTED]> wrote: >From: Patrick Fuchs <[EMAIL PROTECTED]> >Reply

Re: [gmx-users] Very large fluctuations in dg/dl

ohn Chodera <[EMAIL PROTECTED]> | Mobile: 415 867-7384 Postdoctoral researcher, Pande lab| Lab phone : 650.723.1097 Department of Chemistry, Stanford University | Lab fax : 650.724.4021 http://www.dillgroup.ucsf.edu/~jchodera -- Date: Mon, 07 May 2007 16:41:26 +0200 Fr

[gmx-users] Very large fluctuations in dg/dl

sd integrator (when I switch to md integrator, I no longer get these warnings) ? Thanks for your answer, Patrick -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place

Re: [gmx-users] Creation of an index file with seperate lipid leaflets

mx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ Patrick FUCHS Equipe de Bioinformatique G

Re: [gmx-users] can we calculate chemical shifts

@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- _____

Re: [gmx-users] Please Help: Still facing problems with installing Gromacs 3.3.1 on SGI Irix

#x27;t post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ___ Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire

Re: [gmx-users] Compilation problem on SGI ORIGIN 3800

David van der Spoel a écrit : Patrick Fuchs wrote: Hi gmx users, I'm trying to compile gromacs in // on an SGI ORIGIN 3800. For the monoCPU version it went well (thanks to very good advices on previous E-mails of the gmx list), but for the parallel version, I encountered a problem.