Re: [gmx-users] force field parametrs for Mn2+

that contains force field parameters for Mn 2+ . Thanks -- - Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Raffaele Scientific Institute Biomolecular NMR Laboratory Dibit2 Basilica 3A2 Via Olgettina 58 20132 Milano Italy Tel: 0039

Re: [gmx-users] MM-GB/SA analysis in Gromacs

in advance and best regards Anna -- - Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Fondazione Centro San Raffaele Centro di Genomica Traslazione e Bioinformatica Biomolecular NMR Laboratory Dibit2 Basilica 3A2 Via Olgettina 58 20132

[gmx-users] different checkpoint from remd after crash

and -- - Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Fondazione Centro San Raffaele Centro di Genomica Traslazione e Bioinformatica Biomolecular NMR Laboratory Dibit2 Basilica 3A2 Via Olgettina 58 20132 Milano Italy Tel: 0039-0226434348 Fax: 0039-0226434153 http://sites.google.com/site

Re: [gmx-users] different checkpoint from remd after crash

have a full set of matching .cpt files, but not with consistent names. Use gmxcheck to see the times. Mark On Fri, Apr 19, 2013 at 3:24 PM, andrea spitaleri spitaleri.and...@hsr.itwrote: Hi there, I am performing a remd (8 replica) using gromacs-4.5.3 Unfortunately, the job crashed

[gmx-users] pdb2gmx -ter with cyclic peptide

and -- - Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Raffaele Scientific Institute Biomolecular NMR Laboratory Dibit2 Basilica 3A2 Via Olgettina 58 20132 Milano Italy Tel: 0039-0226434348 Fax: 0039-0226434153 http://sites.google.com

Re: [gmx-users] PLUMED plugin in gromacs for protein system

-- - Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Raffaele Scientific Institute Biomolecular NMR Laboratory Dibit2 Basilica 3A2 Via Olgettina 58 20132 Milano Italy Tel: 0039-0226434348 Fax: 0039-0226434153 http://sites.google.com/site

[gmx-users] xpm2ps tick display

= 16 y-font = Times-Roman y-tickfontsize = 10 y-tickfont = Helvetica Any help_?? thanks in advance andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute Center of Genomics, BioInformatics and BioStatistics c/o DIBIT

Re: [gmx-users] Converting 2-d molecule to 3-D

/users.php -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153

[gmx-users] continuing a MD simulation on different architectures

and generating the new tpr on my cluster. I did it and it runs, however I was wondering about the physical and chemical reliability. thanks in advance Regards andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR

Re: [gmx-users] continuing a MD simulation on different architectures

was wondering about the physical and chemical reliability. thanks in advance Regards andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http

Re: [gmx-users] xvg plotting

*To:* gmx-users@gromacs.org *Subject:* [gmx-users] xvg plotting Hi, I am a new user in gromacs and i would like to create a plot from several .xvg files. Can anyone guide me through the process? Thank you in advance N.V. -- - Andrea

Re: [gmx-users] gnuplot

-- - Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Raffaele Scientific Institute Biomolecular NMR Laboratory Dibit2 Basilica 3A2 Via Olgettina 58 20132 Milano Italy Tel: 0039-0226434348 Fax: 0039-0226434153 http://sites.google.com/site/andreaspitaleri/ http://www.linkedin.com

Re: [gmx-users] angle between two domains connected at a hinge

-- - Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Raffaele Scientific Institute Biomolecular NMR Laboratory Dibit2 Basilica 3A2 Via Olgettina 58 20132 Milano Italy Tel: 0039-0226434348 Fax: 0039-0226434153 http://sites.google.com/site/andreaspitaleri/ http://www.linkedin.com

[gmx-users] Mn parameters

. Previous post are: http://www.gromacs.org/component/option,com_wrapper/Itemid,165/ and http://www.gromacs.org/component/option,com_wrapper/Itemid,165/ Thanks in advance Regards andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific

Re: [gmx-users] Mn parameters

Hi all, sorry for the previous wrong links (Thanks to Mark): http://www.gromacs.org/pipermail/gmx-users/2002-April/001333.html http://www.gromacs.org/pipermail/gmx-users/2002-March/001000.html http://www.gromacs.org/pipermail/gmx-users/2006-July/022999.html Regards, andrea andrea spitaleri

[gmx-users] benchmark: buying a new cluster

, Regards andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153

Re: [gmx-users] how to edit pdb file

PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ Tel: 0039

[gmx-users] 4.0_beta1: 1 particles communicated to PME node 9 are more than a cell length out of the domain decomposition cell of their charge group

-dd 4 4 4 option). I hope this help in gmx debugging Regards, andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ Tel: 0039

[gmx-users] 4.0_beta1: 1 particles communicated to PME node 9 are more than a cell length out of the domain decomposition cell of their charge group

Hi again, in addition to the previous post, 4.0_beta1 crashes using 27 cpus and option -dd 3 3 3, whereas it goes fine using 24 cpus and not -dd option. any clue? Regards, andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific

[gmx-users] remd and nmr

into gromacs one of this structure (the best in procheck_nmr) and to see whether the REMD simulation might explore also the other configurations found by cns and give much more clue on the relative stabilty. Any suggestion? thanks in advance andrea -- --- Andrea

[gmx-users] problem running posre

a simulation with no position restraints the runs goes fine. I tried using posrefc 1000 and lower (200). Same result. Any suggestion? Regards andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina

[gmx-users] explicit hydrogen-bond

thanks andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom

Re: [gmx-users] explicit hydrogen-bond

http://www.gromacs.org/mailing_lists/users.php -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom

[gmx-users] gmxcheck and trjconv

-- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ --- ___ gmx-users mailing list

Re: [gmx-users] gmxcheck and trjconv

... gmx version 3.3.1 Regards andrea David van der Spoel wrote: andrea spitaleri wrote: Hi all, silly question. I have checked a trr with gmxcheck and I get this output below: Item#frames Timestep (ps) Step701 Time701 Lambda 701 Coords

Re: [gmx-users] gmxcheck and trjconv

Hi, however in md0.log the right time is reported (69 and not 70) and David van der Spoel wrote: andrea spitaleri wrote: Hi all, silly question. I have checked a trr with gmxcheck and I get this output below: Item#frames Timestep (ps) Step701 Time70

Re: [gmx-users] coordination number of ion: rdf integration

volume should be 10x10x10? I cannot figure out how did you retrieve this conclusion. Thanks for your help anyway, Regards Andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano

[gmx-users] PCoorA and Energies

in advance Regards, andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom

[gmx-users] rdf bug in 3.3.1 depending on the gcc?

10.2 2.6.18.2-34-default I did not find any entry in the bugzilla. Thanks Regards, Andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom

Re: [gmx-users] rdf bug in 3.3.1 depending on the gcc?

Hi, okay I will submit the bugzilla. Thanks Regards, andrea David van der Spoel wrote: andrea spitaleri wrote: Hi all, I have suspicious that g_rdf is bugged or at least it has a problem depending on the machine type. In one pc works and in another it hangs in Reading frame 0. 0.

[gmx-users] ion contact: rdf does not tend to 1

-homogeneous situation?. In few words, after few nm there are not oxygen atoms interacting with the ion. Thanks Regards andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano

Re: [gmx-users] splitting of chains

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 -- --- Andrea

Re: [gmx-users] Prot_prep_problem

or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http

Re: [gmx-users] Prot_prep_problem

I apology for the incorrect spelling of your name ... I have an automatic reply format which sometimes does weird stuff ... Sorry Prasenjit, really. Regards andrea andrea spitaleri wrote: HI Pkmukher, I use to use opls for nmr structures in order to keep the all-hydrogen in the protein

[gmx-users] g_mindist -pi option

this value or is it pbc artefact? Thanks in advance Regards, and ps. gmx3-3-1 compiled on suse-10.2 gcc-v 4.1.2 -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http

Re: [gmx-users] g_mindist -pi option

nm. Any clue? thanks again Regards andrea andrea spitaleri wrote: Hi there, I have a complex protein-peptide in a box 6.5 6.5 6.5 with a starting periodic image of 3.0 nm, using PME and rlist=rvdw=rcoulomb=0.9. Now, I use to check the pi dist during my simulation in order to make sure

Re: [gmx-users] g_mindist -pi option

://www.gromacs.org/mailing_lists/users.php -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom

Re: [gmx-users] g_mindist -pi option

the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http

Re: [gmx-users] does gromos force field can explain pi-pi interaction

Interactions Chemistry - A European Journal Volume 8, Issue 13 , Pages 2860 - 2867 Gianni Chessari, Dr. 1, Christopher A. Hunter, Prof. 1 *, Caroline M. R. Low, Dr. 2, Martin J. Packer, Dr. 1, Jeremy G. Vinter, Dr. 2, Cristiano Zonta Regards andrea -- --- Andrea

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

] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Andrea Spitaleri Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom

Re: [gmx-users] cyclic peptides

PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom

Re: [gmx-users] additional peptide bond: cyclic peptides

PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom

[gmx-users] copper cluster bond to histidines

in a second study. Any suggestion, comments and anything else are very welcome. Thanks in advance Regards andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) Tel

Re: [gmx-users] copper cluster bond to histidines

-- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153 http://sites.google.com/site/andreaspitaleri

Re: [gmx-users] xtc corrupted during REMD

. Are all you xtc corrupted or only some? Are those which are corrupted all corrupted on the same frame or different ones? Roland Andrea Spitaleri PhD Dulbecco Telethon Institute Center of Genomics, BioInformatics

Re: [gmx-users] Error during PUMED installation for GROMACS-4.5.3

//.deps/*.Po': No such file or directory - DONE! -- / - Thanks and regards /Bipin Singh/ / / / -- - Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Raffaele Scientific Institute Biomolecular NMR

Re: [gmx-users] OPLS-AA parameters for Phospho-threonine and serine

Hi, Have look here: http://haddock.science.uu.nl/services/HADDOCK/library.html The ff used by HADDOCK is oplsx derived from opls. Maybe you can exploit them as starting point. Hope it helps And Martin, Erik W erik.mar...@stjude.org ha scritto: I've searched the literature and internet and

[gmx-users] nstcalclr bug?

couldn't find the reason of this behaviour. is this a bug or am I doing wrong somewhere?? thanks for any helps and Andrea Spitaleri PhD D3 - Drug Discovery Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 -- gmx-users mailing listgmx-users

Re: [gmx-users] Lie method for binding free energy calculations

Hi, You can email me we have a tool for mmpbsa with gromacs Andrea Messaggio inviato dal mio ASUS MeMO Pad Justin Lemkul jalem...@vt.edu ha scritto: On 10/25/13 11:43 AM, Sajad Ahrari wrote: is AMBER facilities the only way of approaching MM-PBSA calculations? could you lead me to any