[gmx-users] simulation crash

arts. IMHO, if there was a problem with the system the simulation should never restart, isn't? any clue? Hope I have been clear Best Andrea -- Andrea Spitaleri PhD Computational mOdelling of NanosCalE and bioPhysical sysTems - CONCEPT Lab ISTITUTO ITALIANO DI TECNOLOGIA Via Morego 30,

[gmx-users] bond sequence and improper angles

. Thanks Andrea -- Andrea Spitaleri PhD Computational mOdelling of NanosCalE and bioPhysical sysTems - CONCEPT Lab ISTITUTO ITALIANO DI TECNOLOGIA Via Morego 30, 16163 - Genova, Italy http://it.linkedin.com/in/andreaspitaleri https://www.researchgate.net/profile/Andrea_Spitaleri https://iit.it

[gmx-users] Ris: MM/PBSA

Please refer to our mailing list https://groups.google.com/forum/m/?utm_medium=email&utm_source=footer#!forum/gmxpbsa Best Messaggio originale Oggetto: Re: [gmx-users] MM/PBSA Da: "Kingsley Theras Primus Dass ." <105726...@gms.tcu.edu.tw> A: gmx-us...@gromacs.org CC: sure

Re: [gmx-users] Visualization of xtc file

ro and .xtc files of my complex by VMD but when i load first .gro and then .xtc files in vmd , it has so high motion , such that no molecules are viewable. Would you please help me how can i view it? ThanksFarial Sent from Yahoo Mail for iPhone -- Andrea Spitaleri PhD Computational mOdell

Re: [gmx-users] Makeing movies using VMD

x27;t post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Andrea Spitaleri PhD Computational mOdelling of NanosCalE and bioPhysical sysTe

[gmx-users] Ris: position restraint single atom

How Larger? I used 1000 Messaggio originale Oggetto: Re: [gmx-users] position restraint single atom Da: Justin Lemkul A: gmx-us...@gromacs.org CC: On 2/15/17 9:33 AM, Andrea Spitaleri wrote: > Hi there, > > I have a dsDNA and I'd like to restraint just two ato

[gmx-users] position restraint single atom

elcome. Thanks and -- Andrea Spitaleri PhD Computational mOdelling of NanosCalE and bioPhysical sysTems - CONCEPT Lab ISTITUTO ITALIANO DI TECNOLOGIA Via Morego 30, 16163 - Genova, Italy https://iit.it/research/lines/computational-modelling-of-nanoscale-and-biophysical-systems cell: +39 3

[gmx-users] position restraint single atom

elcome. Thanks and -- Andrea Spitaleri PhD Computational mOdelling of NanosCalE and bioPhysical sysTems - CONCEPT Lab ISTITUTO ITALIANO DI TECNOLOGIA Via Morego 30, 16163 - Genova, Italy https://iit.it/research/lines/computational-modelling-of-nanoscale-and-biophysical-systems cell: +39 3

Re: [gmx-users] Protein-DNA_ligand simulation.

The protocol is generally the same. -Justin -- Andrea Spitaleri PhD Computational mOdelling of NanosCalE and bioPhysical sysTems - CONCEPT Lab ISTITUTO ITALIANO DI TECNOLOGIA Via Morego 30, 16163 - Genova, Italy https://iit.it/research/lines/computational-modelling-of-nanoscale-and-biophysical-sy

[gmx-users] Post-doctoral position in Computational Physics

the theory and modeling for molecular simulation. More information: https://beta.iit.it/careers/openings/opening/81-post-doctoral-position-in-computational-physics Best and -- Andrea Spitaleri PhD Istituto Computational mOdelling of NanosCalE and bioPhysical sysTems - CONCEPT LabItaliano di

Re: [gmx-users] Calculate NMR shift from simulation

different solvents: http://pubs.acs.org/doi/abs/10.1021/jm701194r http://pubs.rsc.org/en/Content/ArticleLanding/2012/CE/C2CE25941A#!divAbstract http://pubs.rsc.org/en/Content/ArticleLanding/2004/CE/b407163h#!divAbstract HTH Best and Andrea Spitaleri PhD D3

Re: [gmx-users] GMXPBSA

Hi, Please have look here: GMXPBSA 2.1: A GROMACS tool to perform MM/PBSA and computational alanine scanning http://www.sciencedirect.com/science/article/pii/S0010465514003154? Contact me in private if you need help Best And Il 20/lug/2015 16:19 Urszula Uciechowska ha scritto: Dear gromacs

Re: [gmx-users] MD simulation of metalloprotein

amber -Justin -- Andrea Spitaleri PhD D3 - Drug Discovery & Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 http://www.iit.it/en/d3-people/andrea-spitaleri.html ORCID: http://orcid.org/-0003-3012-3557 -- Gromacs Users mailing list * Please s

Re: [gmx-users] MMPBSA & GMXPBSA 2.1

/home/user1/Research/Software/DEMO/EXAMPLE1/P53. Exiting... -- Thanks for the help! Thomas -- Andrea Spitaleri PhD D3 - Drug Discovery & Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 http://www.iit.it/en/d3-people/an

Re: [gmx-users] Spacial density map

-requ...@gromacs.org. -- Andrea Spitaleri PhD D3 - Drug Discovery & Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 http://www.iit.it/en/d3-people/andrea-spitaleri.html ORCID: http://orcid.org/-0003-3012-3557 -- Gromacs Users mailing list * Please sea

Re: [gmx-users] MMPBSA with GROMACS: a new revised tool

t; The tool can be used upon request. Feel free to contact me. > > Best > > and > > > -- > --- > Andrea Spitaleri PhD > D3 - Drug Discovery & Development > Istituto Italiano di Tecnologia > Via Morego, 30 16163

Re: [gmx-users] How to efficiently fix pbc trajectories problems for VMD using

Hi there, have look to arrange_objects.tcl in http://people.sissa.it/~xbiarnes/tools.php. That could be useful for your task. and -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Vito Genn