Re: [gmx-users] gromacs analysis performance on a dual core suse box.

ry another kernel scheduler (see the kernel option elevator), but this will be a compromise between responsiveness and throughput. Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA,

Re: [gmx-users] Position restraints on a lipid bilayer

aining on x, not cnostraining on y, and just constraining in z. Yours, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352

Re: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling

y any hazard constraints= all-bonds if so, could you check if the run has the error with h-bonds? In my case that solved the issued with the error message. I suspect a rounding problem but i have not figured out it yet (not really searched for, btw). Cheers, Stéphane -- Sté

Re: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling

Berk Hess a écrit : Is the fix committed already, i cannot get it from the current cvs repository? Cheers, Stéphane Yes, it is: revision 1.57.2.7 of pbc.c. It just adds "2*" in front of BOX_MARGIN. Berk. ok, found, forgot to add the 3.3 branch tag... Thanks for the fix. -

Re: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling

-- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901

Re: [gmx-users] problem regarding insertion of protein into lipidbilayer

e beginning. Both info at http://moose.bio.ucalgary.ca/index.php?page=Programs Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 65

Re: [gmx-users] protein/membrane simulation parameters

side will enter the top of the box, on the extracellular side), this is another good reason to not disturb the simulations. You will probably get more input on this, but at least you have some arguments ... Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.o

Re: [gmx-users] RE : long-term drift and crash

02 or - constraints = all-bonds, dt = 0.004 but not a combination of both. Constraining all-bonds is *merely only* for getting a bigger time step for md, but for regular simulations, i would definitely only constrain h-bonds and use dt=0.002. Cheers, Stéphane -- Stéphane Téletchéa, P

Re: [gmx-users] dummy atom definition prob in FEP

heers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (

Re: [gmx-users] Implicit solvent simulation

nt on this from the core developpers of GROMACS. I'm not trying to get any grief here, if you consider this a non-issue, please ignore the message, that'll be enough to me. Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique In

Re: [gmx-users] Segmentation fault after dt=2fs

bonds" instead of none should solve you problem. Consider also coupling counter-ions and solvent as mentionned by Justin A. Lemkul. Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.f

Re: [gmx-users] Segmentation fault after dt=2fs

bonds" instead of none should solve you problem. Consider also coupling counter-ions and solvent as mentionned by Justin A. Lemkul. Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.f

Re: [gmx-users] Implicit solvent simulation

about the implicit solvent simulation to protein. Thank you. There is no Generalised-Born approach implemented (at least available) but you may consider reaction field. See chapter 7, paragraph "Electrostatics and VdW". Cheers, Stéphane -- Stéphane Téletchéa, PhD.

Re: [gmx-users] Less than Graceful

as. As a sidenote, you'll also find it precompiled on Mandriva, in the contrib section. Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél :

Re: [gmx-users] get_index

wn (think about maintenance ...). Hope this helps, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France

Re: [gmx-users] A few general questions on Gromacs

atever the failure reason) 1 or 255 ... This is a rough verification but in a first rapid approach, you can be sure to not launch the next step if exit status !=0 :-) Hope this helps, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique In

Re: [gmx-users] A few general questions on Gromacs

you can easily generate a *big* box of water but you'll not really benchmark the system even with such a big system if your interconnection is not fast enough (i.e. you have fast network *and* low latency, gigabit for instance is not very efficient for a good scaling). Cheers, Stéphane --

Re: [gmx-users] RNA ffgmx.hdb problems

types properly). Happy hacking :-) Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France

Re: [gmx-users] Stuck --> unstuck ...

David van der Spoel a écrit : Stéphane Téletchéa wrote: I've found out where the problem lie (at least one of ...). Small reminder: i've tried to setup a system consisting of HIV protease + one ligand on a water box. I used the excellent protocol from John E. Kerrigan (Drug-enzym

[gmx-users] Stuck --> unstuck ...

ook at on the system (equilibration, rmsd, temperature, better minimisation if possible, and since it'll be on the wiki, it will be easier to comment), but i think this was important to share already. Thanks a lot in advance for comments, Stéphane -- Stéphane Téletchéa, PhD.

[gmx-users] Small detail for the gromacs signature ...

t an increasing number of signatures while answering. As ai said, small detail. Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 13

[gmx-users] Stuck ...

Mark Abraham a écrit : Stéphane Téletchéa wrote: While switching from NVT to NPT, i'm crashing my simulation. The error message seen is (repeated 10 times, then mdrun aborts): # Step 1 Warning: pressure scaling more than 1%, mu: -1.59647e+20 -1.59647e+20 -1.59647e+20 Correcting in

[gmx-users] pdb2gmx -merge option take a *very* long time, and doesn't work ...

la? Cheers, Stéphane (same message as already sent but with a compressed pdb). -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en

Re: [gmx-users] Strange error from my simulation

up, a GoodPractice section will be a must :-) Thanks for the advice, i'm still searching why it crashes (i'll go earlier in the system setup and see if i can change something). Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique

Re: [gmx-users] Strange error from my simulation

7;m reading the list and trying fo figure out first, before posting :-) Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 7835

Re: [gmx-users] What molecule generator should be used if using GROMOS Force Field?

Mark Abraham a écrit : Stéphane Téletchéa wrote: WU Yanbin a écrit : Hi, Everyone, If I use GROMOS force field, what molecule generator, specially the topology generation, should I use (just like for gromacs force field, there is PRODRG)? I have tried to convert gromacs topology to

Re: [gmx-users] What molecule generator should be used if using GROMOS Force Field?

Sincerely, WU Yanbin The manual is downloadable for free: http://www.gromacs.org/gromacs/documentation/documentation.html You can even have a look at it online: http://www.gromacs.org/external/online-reference-manual.html Have a good lecture, Stéphane -- Stéphane Téle

Re: [gmx-users] How to check memoryuse limit?

try also to use the double version of the program (genbox_d instead of genbox), allocate swap on the machine (man mkswap), or use a computer having more memory to create your input file. Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique

[gmx-users] Strange error from my simulation

o understand why the switch to NPT fails. Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France

[gmx-users] Strategy for chaining jobs using different mdp parameters (long)

ience, Stéphane Joining the two mdp parameters in case the chaining setup needs additionnal parameter: pr1 is for the NVT simulation, pr2 is for the NPT simulation, i'm not using the same pr for the different pr steps, but this should not be a problem for the "generic" way of cha

Re: [gmx-users] Testing Gromacs

, but it may be too specific (using LAM/MPI on a sge batch system). Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352

Re: [gmx-users] same simulation, different results

reported by Robert Duke on the AMBER mailing list a while ago. Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en

Re: [gmx-users] problem with grompp and atomtype

proDRG beta 2.5 mentionning gromacs 96.1 but for now i have no idea about the forcefield used, its validation state, and my question to Dr. van Aalten about this beta server version has not been answered yet (if someone on the list has an explanation, i'm opened to explanations). Cheers,

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

d for reaction-field (not generalized) is 61 for SPC water (referring to Heinz, van Gunsteren & Hunenberger, J Chem Phys 2001, 115, p1125-1136). Is this value a special case for 'generalized-reaction-field' ? Thanks in advance for clarifications. Stéphane -- Stéphane Téletchéa, PhD.

Re: [gmx-users] Unable to swith from NVT to NPT

Mark Abraham a écrit : Stéphane Téletchéa wrote: I'm probalby doing something wrong but since neither the manual nor the mailing list has driven me to the correct answer, i'm asking you the problem. Thanks in advance for you answers and time. ... Using grompp here and supplying

[gmx-users] Unable to swith from NVT to NPT

Source code file: enxio.c, line: 364 Fatal error: Could not find energy term named 'Pcoupl-Mu-XX' --- Please note the same setup with full NPT (Pcoul Berendsen every time) works ... Thanks again for your comments and explanatio

Re: [gmx-users] How to preserve the original sequence number

list for g_desort, see for instance: http://www.gromacs.org/pipermail/gmx-users/2007-January/025584.html Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert

[gmx-users] DNA Helicoïdal Plots over time

inside the scripts (as recommended on the web page) in case you'll have some doubts about parameters. Hoping this will help you analyse faster your DNA trajectories, Stéphane Téletchéa -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique In

Re: [gmx-users] time estimation script

is not very important but from experience there is attention to port to it :-) (if there is a big discrepancy, you'll need to find why) Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.f

Re: [gmx-users] restarting a sorted shuffled trajectory

This said, shuffling and sorting my runs gives me 100% efficiency to 4cpus = they run 4x as fast as they do on a single node. I can't come anywhere near that with plain runs. Thanks a lot for your time and answers, Stéphane -- Stéphane Téletchéa, PhD. http://www.ste

Re: [gmx-users] time estimation script

directly, with a different rule if it is gromacs 3.2.1 or 3.3+. The attached program itself creates data files in a destination dir where a batch file can be used for seing the datas with xmgrace. (Of course i have also a script for producing it ;-). Cheers, Stéphane -- Stéphane Téletchéa, P

[gmx-users] restarting a sorted shuffled trajectory

-np 4 Thanks a lot for your comments/advices. Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-

Re: [gmx-users] pdbgmx warning long bond

side of the box and terminates on the other side. I've explained in detail how to proceed to correct this, please have a look at my message from "30.11.2006 17:57". Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique e

Re: [gmx-users] LINCS error during mdrun

h. I wish I had a dollar for every time I've given the above advice for a LINCS error! Mark Set up a donation page :-) -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Dom

Re: [gmx-users] Query to display Gromacs compile time settings?

tion flags (and should be optimal for a Linux-based cluster environment) Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 89

Re: [gmx-users] Free energy calculation, parallel or sequential lambda runs ?

sume delta_lambda is small but different from 0. Am I missing anything? When you talk about "sequential" run, do you mean no equilibration for each lambda? (there I do see a problem). No, using equilibration between each lambda, but i was mixing both cases. Ignacio Thanks for your ans

Re: [gmx-users] Free energy calculation, parallel or sequential lambda runs ?

ke your advices into account. Best wishes, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France

[gmx-users] Free energy calculation, parallel or sequential lambda runs ?

manual, the Dill's group tutorial, the chapter from Leach, and some other publication from Aqvist, but still i'm not completely convinced of the procedure). Yours, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome

Re: [gmx-users] I need 256 lipids ...

David van der Spoel a écrit : Stéphane Téletchéa wrote: editconf -f dppc64.pdb -o dppc64_pbc.pdb -pbc But unfortunately, some lipids are not imaged (at least 18, 25 and 53). I tried using trjconv but it needs a topol.tpr that i don't have :-( Any hint ? Stéphane It requires some m

Re: [gmx-users] I need 256 lipids ...

David van der Spoel a écrit : Stéphane Téletchéa wrote: Hello, I'm willing to simulate a membrane protein, and to gain lipid equilibration time, i'm using either Dr Tieleman's lipids or Dr Vattulainen's lipids (dppc 128 / dppc64). In order to fully surround my protei

[gmx-users] I need 256 lipids ...

ds ? I'm willing to do a full automated process for the lipids, this is why i did use genconf. I'm actually trying to build manually the lipid bilayer, but since i'm not sure whether i'll use dppc, dmpc, popc, i'm still searching for an automated method. Thanks a lo

Re: [gmx-users] pdb2gmx with force field option

it: http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis I have also a script that does automatize it completely, but it it not for all purpose actually, so i'll share it later. Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathéma

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

hould get what you want. HTH Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cede

Re: [gmx-users] L-BFGS energy minimization wrong!

el and van Maaren, JCTC, 2006, 2, 1-11). Try using regular vdw radius of 1.4 nm. I would use: coulombtype = PME rlist = 0.9 rcoulomb= 0.9 rvdw= 1.4 Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathém

Re: [gmx-users] strange new H-H bond formation during MD

macs and/or vmd (plot the bond versus distance while using vmd, both use xmgrace in the end). BTW, you could use my modified graphlabel.tcl routine to display atom names under vmd + xmgrace: http://www.steletch.org/spip.php?article11 Cheers, Stéphane -- Stéphane Téletchéa, PhD.

Re: [gmx-users] Ambconv package

/ (found via the 'search' option). Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas ced

Re: [gmx-users] Recover corrupted files from DVD

under /mnt/iso (trajconv may help ?). By chance it is possible that only some frames only are missing or corrupted, and you should be able te recover most of the rest (and reconcatenate them). Best regards, Nuno I hope it'll help you, Cheers, Stéphane -- Stéphane Téletch

Re: [gmx-users] single and double

the goal. Thanks. Chris. Cheers, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, F

Re: [gmx-users] Archiving all the simulation data

think they'll become next Christmas 'must have', so price may drop at least by a factor of 2 within one year), but again, it depends on the budget and urgency. Yours, Stéphane T. -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informa

Re: [gmx-users] Question about Athlon 64 4800+ x2 (poor performance)

n the list. Regards, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (33) 1

Re: [gmx-users] topol.tpr made for 2 nodes while mdrun expected 8

rning off HT (in the bios) and considering your dual-cpu for what they are dual CPUs. You'd get better calculations figures and better scalability. Use therefore -np 2. My 0.02 cents. Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématiq