[gmx-users] NVE of water

coupling tc_grps = system tcoupl = no ;nose-hoover tau_t= 0.1 ref_t= 300 ;Pressure coupling pcoupl = no optimize_fft = yes Any suggesions are really welcome. Thank you. Regards, Andrea

Re: [gmx-users] NVE of water

Thank you for your hints. I'll give it a try right now. Regards, Andrea 2010/3/1 Berk Hess > Hi, > > Shake is not relevant for water and also a time step of 2 fs should be > fine. > The cut-off's are the problem. You have a buffer size of 0.1 nm, > which is alre

Re: [gmx-users] pdb & gro files

I don't think the atom number is the problem. I also have systems with more than 9 atoms, and in the gro file the atom number after 9 is reset to 0, but that was never a problem for the simulations. I would check the parameters again, but I don't have a more exact answer to your problem. 2

R: [gmx-users] Supercomputing Center

Hi there, for european users you may think to apply to hpc-europa (http://www.hpc-europa.eu/) and http://www.deisa.eu/ Regards andrea --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132

[gmx-users] copper cluster bond to histidines

le inside of the Cu2+ cluster 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

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

Hi Tsjerk, thanks for the usual useful suggestions! Probably I will go for that, add an harmonic bonds between Cu2+ and N-HIS and I will think how to hand the charges too. Probably this is the less worst solution for now. Thank a lot, Regards andrea Tsjerk Wassenaar wrote: > Hi And

Re: [gmx-users] Dealing with non-aminoacid residues

Hi Pablo, I would write .rtp entries and so on for each monomer. You copy the modified files into your working directory. Have a great day, Andrea 2009/10/6 Englebienne, P. > Hi all, > > > > I’m looking to perform simulations on a series of synthetic co-polymers > conta

[gmx-users] g_sas with pbc

hat I could fill before running the analysis? 3)Should I use another type of box? Trasform the trajectory with some pbc keywords (I've also tried -ur compact without luck)... Thanks in advance and sorry for the long message Andrea ___ gmx-users ma

Re: [gmx-users] Adding ions

have no mismatch of ionsname in different files. I hope this helps. Regards Andrea 2009/11/17 Arden Perkins > I am an undergraduate student and I am still learning to use GROMACS. When > I add my ions to the solution (using genion) by the procedure described in > the funnel web spider tut

[gmx-users] periodic carbon nanotubes

if I have misunderstood the use of periodic_molecules: does the molecule need to be periodic in the 3 X- Y- Z- directions or it can be periodic just along one directions, as in the case of CNT? Any help is more appreciated. Andrea-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.or

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

`./src/kernel//.deps/restraint_waterbridge.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/restraint_zpath.Po': No such file or directory touch: cannot touch `./src/kernel//.deps/testderivatives.Po': No such file or directory touch: cannot touch `./src/k

[gmx-users] g_rmsdist error hi (-1000.000000) <= lo (0.000000)

r: hi (-1000.00) <= lo (0.00) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Could you please help me? Thanks Andrea -- ¯¯¯¯ Andrea Carotti Dipartimento di Chimica e Tecnologia del

[gmx-users] different checkpoint from remd after crash

-- - 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 wrote: Hi there, I am performing a remd (8 replica) using gromacs-4.5.3 Unfortunately, the job crashed for a problem with our cluster

R: [gmx-users] metadynamics

Hi, have look to: http://www.plumed-code.org/ and Andrea Spitaleri PhD Dulbecco Telethon Institute Center of Genomics, BioInformatics and BioStatistics Basilica San Raffaele, 3P 34R Via Olgettina 58 20132 Milano (Italy) http://sites.google.com/site/andreaspitaleri/ www.biomolnmr.org Tel: 0039

[gmx-users] pdb2gmx -ter with cyclic peptide

r any help 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: 0039-02264

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

Re: [gmx-users] hydration layers around protein

etc) hydration layers around a protein. I am curious to know if there is any way to obtain/guess the thickness of this layer. How does one defines the thickness ? Thanks, Bala -- C. Balasubramanian -- *** Andrea Coletta

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

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

Many thanks 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 Olg

R: [gmx-users] Metadynamics with Esential Dynamics Sampling

Hi, I suggest you to visit the plumed webpage and ask to the mailing list. http://www.plumed-code.org/ best and Andrea Spitaleri PhD Dulbecco Telethon Institute Center of Genomics, BioInformatics and BioStatistics Basilica San Raffaele, 3P 34R Via Olgettina 58 20132 Milano (Italy) http

[gmx-users] Dihedral not counted?

missing in the .top file is defined in the .rtp. So I have really no clue what is wrong. I runned pdb2gmx also in debug mode, but the log file seem ok to me. Please give me a good idea :o) Thanks in advance. Andrea ___ gmx-users mailing listgmx-users

Re: [gmx-users] Dihedral not counted?

proper dihedrals, the impropers are OK). Thanks for your help. Andrea RTP.pdf Description: Adobe PDF document TrimerTOP.pdf Description: Adobe PDF document ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx

Re: [gmx-users] Dihedral not counted?

1920 1gd_1 25181924 1gd_1 18192021 1 18192423 1 Cheers, Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the

Re: [gmx-users] Dihedral not counted?

Strange enough, those dihedrals are there, but the dihedral between atoms 2 9 10 and 17 is missing (in the main chain), altough defined in the PS residue (as -CH CH2 CH +CH2). I am still clueless... Greetings, Andrea 2008/10/27 Justin A. Lemkul <[EMAIL PROTECTED]>: > Well, there&

[gmx-users] dihedrals again

2 91011 1 9101116 1gd_1 9101718 1gd_17 10171825 1gd_17 17181924 1gd_1 Best regards, Andrea ___ gmx-users mailing listgmx-users@gromac

[gmx-users] Re: dihedrals again

residues? And are the 2 definitions (with +CH2 and CB at the end) equivalent, taking in acount that we define also an improper of type gi_2 around the CH atom? Cheers, Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman

[gmx-users] Box size

and angles) already when I run pdb2gmx? Thank you in advance for any contribution. Best regards, Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http

[gmx-users] Parameters

Dear users, I have performed a number of simulations using the ffG43a2 ff in 3.2.1 and the following parameters (only a few are given): ; RUN CONTROL PARAMETERS integrator = md tinit= 0 dt = 0.002 nsteps = 125000 comm-mode

Re: [gmx-users] .mdp file

I thought so. Thank you very much! Cheers Andrea 2008/11/10 Justin A. Lemkul <[EMAIL PROTECTED]>: > > > Andrea Muntean wrote: >> >> Hello there, >> >> I have a practical question regarding the mdp file, regardless the >> system to simulate. Before I

[gmx-users] .mdp file

want to run another simulation, with the same input, only with small changes in the mdp file (like number of steps or so), do I have to each time modify the input .mdp and run grompp, or is it enough if I modify mdout.mdp? Best regards, Andrea ___ gmx

[gmx-users] system explodes

! Andrea ___ gmx-users mailing listgmx-users@gromacs.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

Re: [gmx-users] system explodes

Thank you. I will do so. kind regards, Andrea 2008/11/11 Justin A. Lemkul <[EMAIL PROTECTED]>: > > > Andrea Muntean wrote: >> >> I am simulating one chain of PS. The box is produced by pdb2gmx. If I >> run simulations with timestep 0.1 fs up to 0.4 fs every

[gmx-users] PBC only in xy direction

Hi gmx-users, We are using the version 3.3.3. Is there also a posibility to have pbc only in xy direction (as I saw it is possible in Gromacs 4.0)? The manual says nothing about that. Thank you in advance. Best regards, Andrea ___ gmx-users mailing

Re: [gmx-users] PBC only in xy direction

Hi Berk, that is a good idea. Thank you for your answer. Cheers, Andrea 2008/12/11 Berk Hess <[EMAIL PROTECTED]>: > Hi, > > This is not possible in 3.3. > > But in practice you almost never need this, > since it is far more efficient to use pbc=xyz and have a slab of

Re: [gmx-users] Rtp for polymer.

not listed here) I hope that will help. Andrea 2009/2/5 varsha gautham : > Hello justin, > > Am sorry to say that its not useful.But what i mean is that the rtp > constructed manually is building up the polymer and generating topology > files and gro files. > But when i look into

Re: [gmx-users] is there a possibility to convert .gro files directly to PDB?

Hi Andrew, I would do it with editconf with the same options. Regards Andrea 2009/3/11 Andrew Voronkov : > Dear GROMACS users, > is there a possibility to convert .gro files directly to PDB? Or I can do it > only with .tpr? > I've tried gro2pdb -f conf.gro -o conf.pdb >

[gmx-users] Variance in ED

Hi all, perhaps a silly question but i didn't find the correct way to calculate the variance explained by each eigenvec in ED analysis. Could someone point me out to a correct tool/option to use. I'm using gmx v3.3. Many thanks Andrea -- ¯¯¯¯¯¯¯¯ Andrea Carotti Dipar

[gmx-users] Variance in ED

Dear Dr. Wassenaar, many thanks for your kind reply. Andrea -- Andrea Carotti Dipartimento di Chimica e Tecnologia del Farmaco Università di Perugia Via del Liceo, 1 06123 Perugia, Italy phone: +39 075 585 5169 fax: +39 075 585 5161 www http://rpg.unipg.it personal www

[gmx-users] grompp errors

i have a problem with gromp someone can elp me? thanks.. error_grompp Description: Binary data ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/

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

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

also not very clear to me. thanks in advance Regards andrea Berk Hess wrote: > Hi, > > As mdrun will tell you in stderr and md.log when you try continuing, > you will have exact continuation, but not binary identical (which you would > not have anyhow if you use dynamic load

[gmx-users] xpm2ps tick display

-fontsize = 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 BioStati

[gmx-users] extract subsystem energy: problem with mdrun -rerun and LJ(SR)

CNT as well as in the dynamic in vacuo. hope in some answers. Thanks Andrea -- Dr. Andrea Minoia Chemistry of Novel Materials Uneversity of Mons, UMONS Parc Initialis, Avenue Copernic 1 B-7000 Mons, Belgium Mail: mino...@averell.umh.ac.be Tel: +32 65 373859 Fax: +32 65 373861 -- gmx-users mailing

Re: [gmx-users] extract subsystem energy: problem with mdrun -rerun and LJ(SR)

you tell me what else you need? Again, thanks. cheers, Andrea In the absence of information about your ensemble (from your .mdp file or a > description, hint hint) I'd guess it's because you've excluded all the > non-bonded interactions for which you had non-zero paramet

Re: [gmx-users] extract subsystem energy: problem with mdrun -rerun and LJ(SR)

xcl = --- > energygrp_excl = CNT CNT 2) create the index file for the subsystem 3) rerun grompp to create the new tpr for all the system, without energygrp_excl 4) use the new tpr with tpbconv to create the simulation file for the subsystem 5) adjust the trajectory 6) run mdrun -rerun

Re: [gmx-users] xvg plotting

ocess? Thank you in advance N.V. -- ----- 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://ww

Re: [gmx-users] gnuplot

ch Schloar, Prin. K. M. Kundnani College of Pharmacy, Colaba, Mumbai-05. Cont. No. +91 9769051866 -- - Andrea Spitaleri PhD Dulbecco Telethon Institute c/o Raffaele Scientific Institute Biomolecular NMR Laboratory Dibit2 Basilica 3A2 Via Olgettina 58 20132 Milano I

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

Copenhagen -- ----- 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.linke

R: [gmx-users] Conformational sampling

Dear Nisha, have look to the plumed plugin in gromacs: http://merlino.mi.infn.it/~plumed/PLUMED/Home.html you can perform US and Metadynamics calculations. Hope it helps and Andrea Spitaleri PhD Dulbecco Telethon Institute Center of

[gmx-users] remd with disre in gmx4.0.7

range since I am not neither using time nor ensemble averages nor multiple dist restraints. thansk in advance for any help and ---- Andrea Spitaleri PhD Dulbecco Telethon Institute Center of Genomics, BioInformatics and BioStatistics

R: [gmx-users] remd with disre in gmx4.0.7

.2643.4461 – www.sanraffaele.org--- Begin Message --- Hi there, thanks for that. It makes clear. Regards and -------- Andrea Spitaleri PhD Dulbecco Telethon Institute Center of Genomics, BioInformatics and BioStatistics c/o DIBIT Scientific Institute Biomolecula

[gmx-users] gromacs+MOPAC QMMM error

ERSION 4.0.7 Source code file: qmmm.c, line: 191 Fatal error: Ab-initio calculation only supported with Gamess or Gaussian. --- *** What can be the solution?! Thank you Andrea Coletta -- gmx-users mailing listgmx-users@gromacs.org http://lists.g

[gmx-users] xtc corrupted during REMD

; coordinates every 5ps to xtc xtc-precision = 2500 ; xtc-grps= complex; Since the error is happening only for the continuing run, I am just wondering if there is any reason for this. thanks for any help and Andrea

R: [gmx-users] xtc corrupted during REMD

>From the log file I do not see any errors. Everything seems fine. I have free >room space in the hd too :) I am just wondering whether the problem is in the xtc options (precision and writing step) thanks a lot and ---- Andr

Re: [gmx-users] xtc corrupted during REMD

error, but now it sounds a bit strange. I will ask for a long simulation 50ns without extending steps. thanks in advance regards and On 11/22/2010 05:44 AM, Roland Schulz wrote: On Sun, Nov 21, 2010 at 2:05 PM, Spitaleri Andrea mailto:spitaleri.and...@hsr.it>> wrote: Hi, ye

[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

[gmx-users] modify the distance constraints force constant during the simulation

) is there a way to do it with gromacs? I looked carefully in the manual and in the mailing list too, but I couldn't find an option to do this Thanks in advance, Andrea -- Andrea Bortolato, PhD Postdoctoral Associate Dept. of Structural and Chemical Biology Mount Sinai School of Medicine

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

Hi, have look to this: http://stein.bioch.dundee.ac.uk/~charlie/software/pdb-mode/pdb-mode.html I found it very useful regards andrea Wei, Xiupeng wrote: > Dear GMX users, > I have a basic question. I want to put two same box in x direction. > So I need increase the number

[gmx-users] cvs version and position restraints...

ng lists. Any clue about what's going on? Thanks, Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't

Re: [gmx-users] cvs version and position restraints...

Thanks Berk, yes, it was an older version. And I did have separate pme nodes when posre was working. So now I'm trying out the new CVS version. Andrea On Jul 21, 2008, at 1:53 PM, Berk Hess wrote: Hi, There was a bug with PME and position restraints in the CVS version, but that has

[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] T-WHAM for replica

Hello everyone, Does anyone have a script to do T-WHAM analysis of replica exchange trajectories? Any help would be great! Thanks, Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] Polystyrene box

Hello, we are trying to generate a polystyrene box. We have a homemade pdb file, but the residues are not recognised. Have somebody a good pdb file or can tell me what are the standard residues in Gromax? Any other good hints are welcome. Thanks a lot, Andrea

[gmx-users] help with installation

I want to install fftw and gromax in my directory. Everything went ok, fftw was installed without errors. When I configure gromacs I have the error: cannot find fftw3f library. I did use the CPPFLAGS and LDFLAGS. Can somebody help me? Thank you kindly in advance! Andrea

[gmx-users] Preparing polystyrene

rtp file for Polystyrene? Which force filed would be more apropriate (united atoms)? Thank you. Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org

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

cs.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: 0039-0226434348/5622/3497/4922

[gmx-users] .tdb entries for polystyrene (or other linear polymer)

correct parameters in the *.itp file(s). But it is still not clear to me how to define the conectivity between the monomers. Can somebody help me? I saw there are some people simulating polymers with gromacs. Please help! Thank you for any help, Andrea

[gmx-users] monomer's conectivity

y to do so? Regards, Andrea ___ gmx-users mailing listgmx-users@gromacs.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 lis

Re: [gmx-users] monomer's conectivity

hanks again for your help. Best regards, Andrea 2008/10/22 Mark Abraham <[EMAIL PROTECTED]> > Andrea Muntean wrote: > >> I have a *pdb file for a polymer box which I want to use. I defined the >> residues (the first, the last and the inner monomers). >> Pdb2gmx runs

Re: [gmx-users] monomer's conectivity

Thank you. I hope this helps me further. My system is 32 polystyrene chains of 80 monomers. Andrea 2008/10/23 Mark Abraham <[EMAIL PROTECTED]> > Andrea Muntean wrote: > >> Thank you for your answer. >> If I am looking at the PDB standard format and my file, I observe

Re: [gmx-users] monomer's conectivity

It did work. Thank you! Cheers, Andrea 2008/10/23 Mark Abraham <[EMAIL PROTECTED]> > Andrea Muntean wrote: > >> Thank you for your answer. >> If I am looking at the PDB standard format and my file, I observe that I >> have only one number between the type of

[gmx-users] gmxcheck and trjconv

then i use trjconv to dump a configuration file at 70 ps it says: WARNING no output, trajectory ended at 69 Is it normal? I don't mind to extract a configuration file at 69 ps, however i was wondering if this behaviour is normal or whether it is bug. thanks in advance Regards a

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 >> Time

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) >>

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

efficient 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

Re: [gmx-users] peptide coming out of the box

Hi, why do not think about a beginners mailing list or gromacs for dummies? of course this is my humble opinion to you guys and of course I agree with you in searching **always before** in the list archive .. This is just a suggestion ... Regards, andrea Berk Hess wrote: > Maybe

[gmx-users] PCoorA and Energies

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

Re: [gmx-users] mindist during MD

Hi sorry for the poor information. I have used PME with rlist = rcoulomb = rvdw = 0.9 (as I said) and the g_mindist is between the protein-protein system thanks Regards, andrea David van der Spoel wrote: > [EMAIL PROTECTED] wrote: >> Hi all, >> my rlist = rcoulomb = rvdw = 0.

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

115 (prerelease) (SUSE Linux) Suse 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

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 han

[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] genion halted

Hi which gcc have you used for compiling gromacs? I have the same problem in one pc in which I have build gromacs using gcc-4.1 Regards andrea Sampo Karkola wrote: > Dear list, > > the genion program gets halted when I'm trying to replace the solvent > molecules with

Re: [gmx-users] genion halted

gcc-4.0.2 seems ok for gmx-3.3.1 I have also submitted in bugzilla a similar problem with g_rdf Regards andrea Sampo Karkola wrote: > Hi, > > the same one, gcc-4.1. Have you tried with other versions? > > Sampo > > andrea spitaleri wrote: >> Hi >> whic

Re: [gmx-users] genion halted

Hi yes I do use genion and g_rdf properly with 4.0.2 Regards and Sampo Karkola wrote: > Hi, > > so you got genion working with 4.0.2? > > Sampo > > andrea spitaleri wrote: >> gcc-4.0.2 seems ok for gmx-3.3.1 >> I have also submitted in bugzilla a similar pr

Re: [gmx-users] splitting of chains

simulation is to check whether the SS bond is present in your topology in order to be used as it is during the gromacs simulation. Check for the specbond.dat file I hope that it helps Regards andrea özge kül wrote: > After making Md simulation and getting the rmsd,gyration.. analyzing > grap

Re: [gmx-users] Prot_prep_problem

trr in order to analyze for instance the violated NOE. Skip last question, sorry :) Regards andrea pkmukher wrote: > Hello gromacs users, > > > I am facing a particular problem in the preparation of my > protein.I have a NMR derived structure with hydrogens. To > prepare my

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 >

[gmx-users] g_mindist -pi option

nts? is it true 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 (I

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 ord

Re: [gmx-users] g_mindist -pi option

weird behaviour. Besides this, it sounds very strange that the minimum distance goes from 3.0 nm to 0.17 nm and then up to 3.0 in 2 ps ... Therefore vmd and energy profile seem to be consistent with a proper simulation (till now ..) :) Thanks, Regards andrea Miguel Machuqueiro wrote: > At 08:00 AM 6

Re: [gmx-users] g_mindist -pi option

problem, Regards andrea Yang Ye wrote: > On 6/12/2007 7:15 PM, Miguel Machuqueiro wrote: >> At 08:00 AM 6/12/2007, you wrote: >>> Hi again, >>> since I did not get answer I double checked my trr file. In case I >>> calculate the minimum distance of >>>

[gmx-users] psf 2 top

erines). Is there someone that could help me on this topic? Thanks in advance Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before p

[gmx-users] g_cluster questions

, but it asks me however for a group for the LSfitting..could someone explain me this behaviour? Is my procedure correct for my purpose? Is normal that g_cluster does not accept the -fit option? Thanks Andrea -- ¯¯¯¯ Andrea Carotti Dipartimento di Chimica e Tecnologia del

[gmx-users] g_rms

as imaging that it should have 2200 rows and 33 columns, am I wrong? The second question is something that is already been asked before..it could be usefull to obtain the matrix 2200 x 33 in a human readable file. Is it possible without hacking the code? Perhaps using external scripts? Thanks a lot ag

Re: [gmx-users] g_rms

umber of atoms (same structure). During the calculation i can see that it is creating the 2200x33 matrix, but on the rmsd.xvg i find only two columns. From the xpm and dat files i can't extract the matrix (i don't know) to a text file. I hope this could clarify better m

Re: [gmx-users] g_rms

-f 2200.pdb -f2 33.pdb -s ref.pdb -n -o -m -bin I obtain a rmsd.xvg with 2 columns. So, which is the meaning of that value? a mean of all the rmsd calculated for that frame in respect to the other 33 refs? Thanks Andrea -- Andrea Carotti Dipartimento di Chimica e Te

Re: [gmx-users] g_rms

> So does the -Rmat option not produce a human-readable text file? Hi, unfortunately I can't see this option in g_rms. I'm using the v 3.3.1 and also on the reference page online there is not -Rmat. Am i missing something? Thanks Andrea

[gmx-users] xpm to ascii

a step by step guru guide... Thanks Andrea ___ gmx-users mailing listgmx-users@gromacs.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)subscr

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