[gmx-users] Re: Re: calculating dihedral properties

Dear Justin, sorry for the late answer and acknowledgements... Please see below my comments. Anna __ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Giovanni Paolo II, 132 84084 Fisciano (SA

[gmx-users] calculating dihedral properties

best regards Anna -- ______ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Giovanni Paolo II, 132 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +39 089 969603 E-mail: amarabo...@unisa.it Skype: annam1972 Web page: http://www.unisa.it/docenti

Re: Re: [gmx-users] how to deal with LINCS warnings despite prolonged stabilization of the system?

for your experience, can a bad parameterization of the protein ligand influence not only the ligand itself but also the protein determining the starting of LINCS WARNINGS on atoms that apparently are (relatively) far from the ligand? Thanks a lot Anna _____

[gmx-users] how to deal with LINCS warnings despite prolonged stabilization of the system?

terms and comparison with the simulations that went well. I don't see any significant difference (if somebody wants to see, I can provide the files) Thanks a lot Anna -- __ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology

[gmx-users] still dealing with GFP-like chromophore with LINCS warnings

ization, do I have to avoid switching from Berendsen to Parrinello? What do you suggest me to do? Thanks a lot Anna -- __ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Giovanni Paolo II, 132 84084 Fi

[gmx-users] Re: Re: Re: Re: help with a chromophore of GFP

re, but I am not able to find it. Anna ______ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Ponte don Melillo 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +39 089 969603 E-mail: amarabo...@unisa.it Skype: annam1972 "When a m

[gmx-users] Re: Re: Re: help with a chromophore of GFP

general ones already defined in ffbonded.itp. Can this fact contribute for this error? I hope that all is clear; always many thanks for your help, and best regards Anna -- __ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology Univ

[gmx-users] Re: Re: Re: Re: help with chromophore of a GFP

know how to find a way to send you all information. Thanks Anna __ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Ponte don Melillo 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +39 089

[gmx-users] Re: help with chromophore of a GFP

Dear gmx-users, dear Mark, thank you for all the help you are giving me for this subject. I'm still proceeding to my target.. Thanks to your previous suggestions, I was able to parametrize bonds and angles of CFY. Now I'm dealing with dihedrals... In the parameter files derived by Antechamber

[gmx-users] Re: Re: help with chromophore of a GFP

Dear gmx-users, I'm still dealing with my problem of obtaining parameters for my chromophore of the GFP family, in order to treat it as a new residue. I'm trying (VERY hardly) to add missing parameters into ffbonded.itp file for AMBER99SB ff, using those parameters found in files calculated by

[gmx-users] Re: Re: help with chromophore of a GFP

.itp (the kb in kJ mol-1 nm-2) from the data I have? I don't recognize at all the value... I know that this is not strictly referred to Gromacs, anyway could you please tell me at least how can I find information on how to add these parameters properly? Anna _______

Re: [gmx-users] help with chromophore of a GFP

to its > neighbours with normal peptide links. > -- Message: 5 Date: Thu, 21 Mar 2013 11:46:12 +0100 From: Mark Abraham Subject: Re: [gmx-users] help with chromophore of a GFP To: Discussion list for GROMACS users Message-ID: Content-Type: text/plain; charset=IS

Re: [gmx-users] help with chromophore of a GFP

To: Discussion list for GROMACS users Message-ID: Content-Type: text/plain; charset=ISO-8859-1 On Wed, Mar 20, 2013 at 1:01 PM, Anna MARABOTTI wrote: > > >Dear gmx-users, > >it's about two weeks that I'm trying to solve this >problem, and I can't, so I'm as

[gmx-users] help with chromophore of a GFP

Dear gmx-users, it's about two weeks that I'm trying to solve this problem, and I can't, so I'm asking your help. I want to do some MD simulations on a protein of the family of green fluorescent protein. This protein, as you know, has a chromophore (CFY) derived from four residues of the pro

[gmx-users] Re: Re: problem with a complex cofactor

Thank you Justin for your suggestion. I searched into the archive to find something about GFP chromophore before writing to the list, but I did not find anything, I' d try to search better. Anna __ Anna Marabotti, Ph.D. Assistant Professor Depar

[gmx-users] problem with a complex cofactor

advance and best regards Anna -- ______ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Ponte don Melillo 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +39 089 969603 E-mail: amarabo...@unisa.it Skype: annam1972 "When a ma

[gmx-users] conversion of Gromacs trajectories (rhombic dodecahedric), and topologies to Amber format

the trajectory is not in the classic cubic format. This is just for records since it is a recurrent query in the gmx-user archive, still apparently with no solution. Many thanks in any case and best regards Anna -- __ Anna Marabotti, Ph.D. Assistant

[gmx-users] conversion of Gromacs trajectories (rhombic dodecahedric) and topologies to Amber format

anks in advance for your kind answer and best regards Anna -- __ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Ponte don Melillo 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +39 089 969603

[gmx-users] how to convert a dodecahedric trajectory into a triclinic one?

mmand, but I have some trouble in doing it, I don't understand which are the correct flags to use. Could anybody give me some suggestion about this problem? Many thanks in advance and best regards Anna -- __ Anna Marabotti, Ph.D. Assistant

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

ns with another program? Many thanks in advance and best regards Anna -- __ Anna Marabotti, Ph.D. Assistant Professor Department of Chemistry and Biology University of Salerno Via Ponte don Melillo 84084 Fisciano (SA) Italy Phone: +39 089 969583 Fax: +

[gmx-users] PBC treatment: need an explanation

ys to manage the trajectories in order to remove the spikes related to jump across the periodic boundaries? Thank you very much for help, and best regards Anna ____ Anna Marabotti, Ph.D. Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm &quo

[gmx-users] quick question about restart

k you very much Anna ____ Anna Marabotti, Ph.D. Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm "When a man with a gun meets a man with a pen, the man with a gun is a dead man" (Roberto Benigni, about Roberto Saviano) -- gmx-users mailing listgmx-users@gromacs.org ht

[gmx-users] R: Re: several questions about g_hbond -contact

Date: Tue, 21 Feb 2012 15:39:48 -0500 From: "Justin A. Lemkul" Subject: Re: [gmx-users] several questions about g_hbond -contact To: Discussion list for GROMACS users Message-ID: <4f440114.9010...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti

[gmx-users] several questions about g_hbond -contact

o the code, as suggested by somebody...) My final question is, obviously: what is the correct command to provide to obtain what I want, i.e. the number of contacts between the protein and the ligand within a cutoff radius of 0.5 nm? Thanks in advance for your suggestions, and best regards Anna __

[gmx-users] a doubt about pbc nojump or mol or whole

uppose that this system is anomalous only for this fact? Any help would be very appreciated. Many thanks in advance and best regards Anna __ Anna Marabotti, Ph.D. Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm "When a

[gmx-users] R: Re: H-bond lifetime with g_hbond

t; Subject: Re: [gmx-users] H-bond lifetime with g_hbond To: Discussion list for GROMACS users Message-ID: <4e9451dc.6010...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: > Dear gmx-users, > I have a protein with 5 different ligands. For each

[gmx-users] H-bond lifetime with g_hbond

ry much and best regards Anna ____ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Email: anna.marabo...@isa.c

[gmx-users] about periodic image minimum distance

a way to predict the risk of having a similar problem looking at the system BEFORE simulation is made (and time is wasted...), and if it depends on some incorrect setting of the system (maybe some .mpd option?), or not. Thank you very much for your answers. Anna _______

[gmx-users] problem in topology with AMBER99SB

ro -o prot-lig_solv.tpr -p Result: Fatal error: Atomtype n not found 　 What's wrong? Why Gromacs claims that directives are not in correct order? Could you please help me? Many thanks Anna __ Anna Marabotti, Ph.D. Laboratory o

[gmx-users] R: R: Re: g_cluster error in rhombic dodecahedric system

11 18:26:57 +0200 From: Tsjerk Wassenaar Subject: Re: [gmx-users] R: Re: g_cluster error in rhombic dodecahedric system (Mark Abraham) To: Discussion list for GROMACS users Message-ID: Content-Type: text/plain; charset=ISO-8859-1 Hi Anna, On Thu, Jul 21, 2011 at 5:11 PM,

[gmx-users] R: Re: g_cluster error in rhombic dodecahedric system (Mark Abraham)

CS users Message-ID: <4e2836bf.3000...@anu.edu.au> Content-Type: text/plain; charset="iso-8859-1" On 21/07/2011 11:38 PM, Anna Marabotti wrote: > Hi folks > here I am with another kind of error, this time analysing my > trajectory of the rhombic dodecahedron dimeric system w

[gmx-users] g_cluster error in rhombic dodecahedric system

#x27;t know how to manage it. Could the .tpr file I used be the cause of the problem? Could anybody help me please? Thank you so much for your continue support Anna ______ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Com

[gmx-users] R: Re: rhombic dodecahedron and g_sas

tains no charges. As a consequence, all atoms are taken to have zero charge, and thus regarded hydrophobic. Cheers, Tsjerk On Wed, Jul 13, 2011 at 2:35 PM, Anna Marabotti wrote: > Dear all, > once again about this subject (I'm not sure I'll do another simulation in a > r

[gmx-users] rhombic dodecahedron and g_sas

box. Am I true? What can I do? Do I have to convert my trajectory into a rectangular one? Do I have to forgot to calculate SASA in these conditions? Any help will be appreciated... Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinfor

[gmx-users] R:Re: R: Re: g_mindist on rhombic dodecahedron system

e1b08df.1060...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: > Dear Justin, dear all, > following your suggestion I used the command: > trjconv -f prot_boxdodfull.xtc -s prot_boxdodfull.tpr -pbc mol -ur compact > -o prot_boxdodfull_mol.xtc

[gmx-users] R: Re: g_mindist on rhombic dodecahedron system

l 2011 12:24:11 -0400 From: "Justin A. Lemkul" Subject: Re: [gmx-users] Re: g_mindist on rhombic dodecahedron system To: Discussion list for GROMACS users Message-ID: <4e133aab.1030...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: >

[gmx-users] Re: Re: g_mindist on rhombic dodecahedron system

on rhombic dodecahedron system To: Discussion list for GROMACS users Message-ID: <4e133aab.1030...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: > Dear Tsjerk, > thank you very much for your answer. I completely re-analyzed my simulations > an

[gmx-users] Re: g_mindist on rhombic dodecahedron system

e, Jul 5, 2011 at 2:49 PM, Anna Marabotti wrote: > Dear users, > can anybody give me suggestions about my questions below? > Thank you very much > Anna > ____ > Da: Anna Marabotti [mailto:anna.marabo...@isa.cnr.it] > Inviato: lunedl 4 luglio 2011 17.43

[gmx-users] R: g_mindist on rhombic dodecahedron system

Dear users, can anybody give me suggestions about my questions below? Thank you very much Anna _ Da: Anna Marabotti [mailto:anna.marabo...@isa.cnr.it] Inviato: lunedì 4 luglio 2011 17.43 A: 'gmx-users@gromacs.org' Oggetto: g_mindist on rhombic dodecahedron system

[gmx-users] g_mindist on rhombic dodecahedron system

he problem comes from... Anna ______ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via Roma, 64 83100 Avellino Phone: +39 0825 299651 Fax: +39 0825 781585 E-mail: amarabo...@isa.cnr.it

[gmx-users] about periodic image violations

Sorry, I forgot to change the subject of my previous mail. Anna -Messaggio originale- Da: Anna Marabotti [mailto:anna.marabo...@isa.cnr.it] Inviato: martedì 28 giugno 2011 12.09 A: 'gmx-users@gromacs.org' Oggetto: R: gmx-users Digest, Vol 86, Issue 183 Dear Tsjerk, dear all,

[gmx-users] R: gmx-users Digest, Vol 86, Issue 183

wouldn't see violations of the minimal distance. In a rhombic dodecahedron the spatial distribution is much more uniform... Cheers, Tsjerk On Mon, Jun 27, 2011 at 12:48 PM, Anna Marabotti wrote: > Dear gmx-users, > I'm inserting into the discussion about periodic images since I&#

[gmx-users] about periodic images violation

Dear gmx-users, I'm inserting into the discussion about periodic images since I'm experimenting a problem of minimum distance violation too. I'm doing simulations on a dimeric protein (with no covalent bonds between the two subunits) which derives not from a crystallographic structure but from a mo

R: Re: [gmx-users] simulation of a peptide anchored to a support

ute to the discussion! Anna Date: Thu, 19 May 2011 19:17:20 +1000 From: Mark Abraham Subject: Re: [gmx-users] simulation of a peptide anchored to a support To: Discussion list for GROMACS users Message-ID: <4dd4e020.2080...@anu.edu.au> Content-Type: text/plain; charset="iso-8859-1" O

[gmx-users] simulation of a peptide anchored to a support

Anna Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Email: anna.marabo...@isa.cnr.it Skype account: anna

[gmx-users] problem in gmx-users list archive?

please fix this problem? Anna ________ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Email: anna.marabo...@isa.cnr.it Skype acc

R: Re: [gmx-users] numbering of .gro file

:54:38 -0400 From: "Justin A. Lemkul" Subject: Re: [gmx-users] numbering of .gro file To: Discussion list for GROMACS users Message-ID: <4dcd381e.1020...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: > Dear Mark, > thank you al

Re: [gmx-users] numbering of .gro file

Sorry I forgot to change the subject of my previous mail (see below) Anna -Messaggio originale- Da: Anna Marabotti [mailto:anna.marabo...@isa.cnr.it] Inviato: venerdì 13 maggio 2011 15.49 A: 'gmx-users@gromacs.org' Oggetto: R: gmx-users Digest, Vol 85, Issue 101 Dear Mark,

[gmx-users] R: gmx-users Digest, Vol 85, Issue 101

Discussion list for GROMACS users Message-ID: <7690ae4b5380.4dcdb...@anu.edu.au> Content-Type: text/plain; charset="iso-8859-1" On 13/05/11, Anna Marabotti wrote: > > Dear > gmx-users, > > I'm simulating a > homodimeric protein obtained by homolo

R: Re: [gmx-users] numbering of .gro file

Subject: Re: [gmx-users] numbering of .gro file To: Discussion list for GROMACS users Message-ID: <4dcd2471.3020...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: > Dear gmx-users, > I'm simulating a homodimeric protein obtained by homolog

[gmx-users] numbering of .gro file

Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via Roma, 64 83100 Avellino Phone: +39 0825 299651 Fax: +39 0825 781585 E-mail: amarabo...@isa.cnr.it Skype account: annam1972 Web site: http://bioinformatica.isa.cnr.it/anna/ann

[gmx-users] R: Md continuation with cpt

w .edr file in which I could obtain a "coarse-grained" (the sampling was every 5 steps) .edr file in which I could see that the energy values are stable. Any suggestions on this point? Many thanks and best regards Anna -Messaggio originale- Da: Anna Marabotti [mailto:anna

[gmx-users] R: Md continuation with cpt

[gmx-users] R: Md continuation with cpt To: Discussion list for GROMACS users Message-ID: <4db947c0.90...@anu.edu.au> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 4/28/2011 5:47 PM, Anna Marabotti wrote: > Dear Justin, > thank you for your precious help. Yes, the pr

[gmx-users] R: Md continuation with cpt

l" Subject: Re: [gmx-users] Md continuation with cpt To: Discussion list for GROMACS users Message-ID: <4db833db.4050...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: > Dear gmx-users, > since I'm sending my simulations to a

[gmx-users] Md continuation with cpt

continuation? Could somebody help me to find the error? Many thanks in advance and best regards Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via Roma, 64 83100 A

[gmx-users] ffbonded.itp file

, not to each others (no C-C bond) and that oxygen is linked only to sulphur (no O-C bond). Could you please check for these strange interactions, or am I mistakenly interpreting them? Thank you very much and best regards Anna Marabotti -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] R: Re: adding a new residue in the ff

Dear Justin and Tsjerk, thank you very much for your last encouraging words...;-) I don't remember a time in my life where something that I needed, which was very complex to do, was already available...(apart from Gromacs package, of course!) About parameterization: sure I was intended to use the p

[gmx-users] adding a new residue in the ff

ive me some hint to do it correctly, and more generally to manage correctly the whole problem? Thanks a lot Anna Marabotti ______ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CN

[gmx-users] LINCS warning on galactose molecule

, if possible!) have some hints about my problem? Or could it be a problem of galactose topology? Thank you very much and best regards Anna ______ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute

[gmx-users] .cpt and .trr files

precision of the result)? At present I'm keeping he .trr files (which contains all information) only to be sure I can restart a simulation, but I need DESPERATELY free disk space... Thank you very much Anna __ Anna Marabotti,

[gmx-users] Re: disulfide bridge broken during EM

essage-ID: <4d78ce62.2010...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: > Dear all, > I have a PDB file of a protein that is in dimeric form, with an > INTERchain disulphide bridge. However, in their paper the > crystallograp

[gmx-users] disulfide bridge broken during EM

prompt. Any suggestions? Many thanks and best regards Anna Marabotti PS BTW: often when I'm searching in the gmx-users list I see the suggestions to some links (for example in the message in http://lists.gromacs.org/pipermail/gmx-users/2008-March/032662.html Mark Abraham suggests to explor

[gmx-users] where to insert a new include DPOSRES in topology file?

ot; just below the statement for the forcefield. Thank you very much Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via Roma, 64 83100 Avellino Phone: +39 0

[gmx-users] R: gmx-users Digest, Vol 82, Issue 113

s, it will start counting over. Cheers, Tsjerk On Mon, Feb 14, 2011 at 4:52 PM, Anna Marabotti wrote: > Dear Tsjerk, > thank you very much. I really didn't know that the PDB format does not allow > more than residues (in fact, it is the first time I have such a big > sys

[gmx-users] R: visualizing more than 9999 residues...

n, Feb 14, 2011 at 4:29 PM, Anna Marabotti wrote: > Dear gmx-users, > I have a system formed by protein+ligand+lipid bilayer that accounts for > about 10500 residues (56000 atoms). It seems to me that it is not possible > to visualize correctly such a large system with Pymol or VMD,

[gmx-users] visualizing more than 9999 residues....

lem without removing residues. I searched for some hints in the gmx-user list and in Google but I didn't find anything. Thank you very much and sorry for this off-topic question. Anna Marabotti ______ Anna Marabotti, Ph.D. Laborat

Re: [gmx-users] protein+ligand+membrane: which forcefield?

charges properly, which is no small task. -Justin > Many thanks for suggestions and best regards. > > Anna Marabotti -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech

[gmx-users] protein+ligand+membrane: which forcefield?

corrected forcefield instead? I did not understand if the Gromos 53a6 ff was chosen in the tutorial because it is better than 43a1 to manage such systems, or because it is more compliant than 43a1 with Berger lipids parameters. Many thanks for suggestions and best regards. Anna Marabotti -- gmx-use

[gmx-users] Re: Re: segmentation fault while running eneconv

nition of the manual) and stop the program claiming for the lack of the .cpt file, in case of such a mistake... Thanks to all and best regards Anna ____ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food

[gmx-users] Re: segmentation fault while running eneconv

t;4d3ee188.7000...@vt.edu> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > >Anna Marabotti wrote: >> Dear all, >> >> I launched on my system a first simulation of 5 ns, then I prolonged it >> to 50 ns using >> tpbconv -s tpr1_5ns.tpr -

[gmx-users] segmentation fault while running eneconv

do to concatenate my .edr files? Many thanks in advance and best regards Anna Marabotti Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100 Avellino (Italy) Phone: +39

[gmx-users] extending simulations made with version 3.3.3

s etc. Many thanks in advance and best regards Anna Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585

[gmx-users] R: problem with .edr file

, but the .edr was not properly saved. I don't know why this happened: do you think it could be a problem in the Gromacs version, or in the Gromacs installation? Any hint will be very appreciated. Many thanks in advance and best regards Anna __

[gmx-users] problem with .edr file

Many thanks in advance and best regards Anna ____ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Email: anna.marab

[gmx-users] initial velocities analysis

ok at the .log file but I didn't find the information. g_traj generated a very big file, and presently I have some problems to analyze it. How can I see initial velocities? Many thanks and best regards Anna ____ Anna Marabotti, Ph.D. Lab

[gmx-users] Re: stepsize too small: help to solve problem in GROMACS installation

- Original Message - From: Anna Marabotti Date: Thursday, May 27, 2010 16:55 Subject: [gmx-users] Re: stepsize too small: help to solve problem in GROMACS installation To: gmx-users@gromacs.org > Dear Justin, dear all, > sorry for not having seen the warning before asking the question

[gmx-users] Re: stepsize too small: help to solve problem in GROMACS installation

Dear Justin, dear all, sorry for not having seen the warning before asking the question about compilers (just a little justification, however: the warning appears only on the Download page, not on the Installation page; I went directly to the installation page and I did not notice it). The only ot

[gmx-users] stepsize too small: help to solve problem in GROMACS installation

--program-suffix=_mpi --with-gsl --enable-mpi --enable-double && make mdrun -j $NCPU && make install-mdrun Could anybody of you help us for the debugging of this installation? Many thanks again and best regards Anna Anna

[gmx-users] Re: stepsize too small ... but potential energy negative!

on my problem. I also want to thank Luca Mollica for his precious support during these days. Best regards Anna -Messaggio originale- Da: Justin A. Lemkul [mailto:jalem...@vt.edu] Inviato: martedì 25 maggio 2010 15.28 A: Anna Marabotti Oggetto: Re: R: coordinates and topologies of file

[gmx-users] Re: stepsize too small ... but potential energy negative!

Once again thank you very much and best regards Anna ____ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 7815

[gmx-users] Re: stepsize too small ... but potential energ negative!

or GROMACS users Message-ID: <4bfa885b.9040...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: > Dear Justin, dear Luca, > here's the answer to your questions: > - I'm currently using the "classical" forcefield gromo

[gmx-users] Re: stepsize too small ... but potential energy negative!

Dear Justin, dear Luca, here's the answer to your questions: - I'm currently using the "classical" forcefield gromos96 43a1 (choice "0" in pdb2gmx). After producing the topology, the only warning I see from pdb2gmx is this one: WARNING: there were 0 atoms with zero occupancy and 63 atoms with occup

[gmx-users] stepsize too small ... but potential energy negative!

Dear Luca, dear all, thank you for your hints. I made some trials with my systems and these are my answers to your questions: - my system is a protein (with or w/o ligand) in solvent (water SPC). Following your suggestions, I tried to perform an EM on the protein w/o ligand after the editconf step

[gmx-users] stepsize too small ... but potential energy negative!

appens in both cases, so I don't think it's a problem related to the ligand. What do you think about? Could you give me some hint? Thank you very much and best regards Anna ______ Anna Marabotti, Ph.D. Laboratory of Bioinforma

[gmx-users] Re: minimizing ligand only

n, 17 May 2010 12:30:17 -0400 From: "Justin A. Lemkul" Subject: Re: [gmx-users] minimizing ligand only To: Discussion list for GROMACS users Message-ID: <4bf16f19.5000...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wrote: > Dear gmx-users,

[gmx-users] minimizing ligand only

can't understand what to do. Many thanks in advance and best regards Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science - CNR Via Roma, 64 83100 Avellino Phone: +39 0

[gmx-users] MD localized in the active site

x27;t find anything. Could anybody give me some suggestions about this subject, please? Many thanks in advance and regards. Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science

[gmx-users] Re: Re: problems running REMD on grids

it works. Anna Date: Sat, 19 Sep 2009 05:22:16 +1000 From: Mark Abraham Subject: Re: [gmx-users] Re: problems running REMD on grids To: Discussion list for GROMACS users Message-ID: <4ab3dde8.8000...@anu.edu.au> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anna Marabotti wr

[gmx-users] Re: problems running REMD on grids

nts and regards Anna ____ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Email: anna.marabo...@isa.cnr.it Skype ac

[gmx-users] Re: problems running REMD on grids

: [gmx-users] problems running REMD on grids To: Discussion list for GROMACS users Message-ID: Content-Type: text/plain; charset="utf-8" Did you try to remove the "_" from your file name? On Sep 11, 2009, at 14:04, Anna Marabotti wrote: > Dear gmx-users, > I'm try

[gmx-users] problems running REMD on grids

ww.gromacs.org site, but I am still unable to consult the gmx-users archives using a keyword as it was possible in the past. How can I find information in the GROMACS archives? Many thanks and regards Anna Anna Marabotti, Ph.D. Laborator

[gmx-users] R: problems running REMD on grids

I'm re-sending the message below because it seems to me that it has not arrived to the list. Please forgive me in case of duplicate sending. Best regards Anna _ Da: Anna Marabotti [mailto:anna.marabo...@isa.cnr.it] Inviato: venerdì 11 settembre 2009 14.05 A: 'gmx-users@g

[gmx-users] using GROMACS in SDS-water simulations

hanks for help and best regards Anna __ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Skype: annam1972 E-mail: am

[gmx-users] Re: Re: protein in SDS/water

at computers do everything I need, but it would be nice that they could at least suggest me a solution in a less cryptic way when I have such a trivial problem, so I can avoid boring the developers themselves...;-) Thank you to all for collaboration and best regards Anna Anna Marabotti wrote: &

[gmx-users] Re: protein in SDS/water

unclarified question: why genbox did not create by itself all corrections necessary to the original .top file when I used the -ci -nmol options? I added the -p flag but it doesn't change the topology by itself (as it should do, in my opinion). Thank you again Anna _

[gmx-users] Re: protein in SDS/water

SDS 3 ; Include topology for SDS #include "SDS.itp" [ system ] ; Name Protein in water with SDS [ molecules ] ; Compound#mols Protein 1 SOL 36173 SDS 2000 I hope __ Anna Marabotti, Ph.D. Laboratory

[gmx-users] Re: protein in SDS/water

ms perfect for me and apparently it > functions in creating the system. > So why the topology file is not updated by genbox? Or in case, could you > suggest me a better procedure to add > 3.5 M SDS to my protein in water? > > Thank you and best regards > Anna > > I tri

[gmx-users] protein in SDS/water

ank you and best regards Anna I tried to copy the .top file at the end of the message, but it is too big, so please if you need to see it let me know how to send to you. ______ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biolog

[gmx-users] Re: trouble for old/new GROMACS site

ite, I cannot reach its content. I don't know if I'm the only person with this difficulty, could you please check it? Thanks anyway for the link and regards Anna ______ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biolog

[gmx-users] trouble for old/new GROMACS site

had to register to see the content of the site, and I did it, but still I don't see anything in the two sites. Can anyone help me? Thank you Anna ______ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Scie

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