[gmx-users] Trajectory to matrix

Dear all I need to export all MD trajectory's data to a matrix. As column header I'd like to put each atom indentified by residue name and progressive number e.g. LYS-N1 In the rows I'd like to put z coordinate changing in time.   Any  suggestion?   Thanks-- gmx-users mailing listgmx-users@gr

[gmx-users] do_dssp segmentation fault

Dear all I'm experiencing the following error in Gromacs 4.5 with do_dssp Here is the command do_dssp -f md.xtc -s md.tpr -o secondary-structure.xpm -sc secondary-structure.xvg -dt 10 give me the following error segmentation fault How can I fix it? Thank in ad-- gmx-users mailing listgmx-

Re: [gmx-users] do_dssp segmentation fault

On 22/11/2011 7:28 PM, Alex Jemulin wrote: Dear all I'm experiencing the following error in Gromacs 4.5 with do_dssp Here is the command do_dssp -f md.xtc -s md.tpr -o secondary-structure.xpm -sc secondary-structure.xvg -dt 10 give me the following error segmentation fault How can I fix it?

Re: [gmx-users] Trajectory to matrix

On 22/11/2011 7:27 PM, Alex Jemulin wrote: Dear all I need to export all MD trajectory's data to a matrix. As column header I'd like to put each atom indentified by residue name and progressive number e.g. LYS-N1 That will be your job to parse the .gro file suitably and write a header. In t

Re: [gmx-users] Trajectory to matrix

  Where can I download the old version? Thanks Da: Mark Abraham A: Discussion list for GROMACS users Inviato: Martedì 22 Novembre 2011 9:32 Oggetto: Re: [gmx-users] Trajectory to matrix On 22/11/2011 7:27 PM, Alex Jemulin wrote: Dear all >I need to export al

[gmx-users] Force equations of virtual site type 4fdn

Hi all-gmxers The force equations of old virtual site type 4fd were shown in GROMACS manual. But the ones of corresponding new type 4fdn are not shown in new GROMACS manual. Can someone do me a favor to give the force equations? Appreciate any help and thanks in advance! 2011-11-22 Best

Re: [gmx-users] Force equations of virtual site type 4fdn

On 22/11/2011 7:27 PM, xuji wrote: Hi all-gmxers The force equations of old virtual site type 4fd were shown in GROMACS manual. But the ones of corresponding new type 4fdn are not shown in new GROMACS manual. Can someone do me a favor to give the force equations? You will have seen that the

Re: [gmx-users] amber99sb in GROMACS vs amber99sb in AMBER

Hi there, Acpype does the conversion for you and the results from their own testing are here: http://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx For reproducing experimental data I would look in the original force-field publications. Oliver On Mon, Nov 21, 2011 at 8:21 PM, Michael Shirts

[gmx-users] PMF curve

Hello, I have done umbrella sampling for 10ns on 23 windows and g_wham program shows converged histograms and PMF curve. I used the following g_wham command, g_wham -it tpr-files.dat -if pullf-files.dat -unit kCal -o profile.xvg -hist histo.xvg -b 1000 -e 1 I considered first 1ns simulation

[gmx-users] PMF curve

Hello, I got a PMF curve like 0...-2...022. its converged at 22. I have a doubt in the final deltaG value, for this curve the deltaG is 22-2 or 22-0. Regards, Vijay. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archi

[gmx-users] Box in Implicit Solvent Simulations

Hi, I am running simulations using implicit solvent. I am using the pbc = no option in my mdp file, however, I see it the .gro file that gromacs is creating a box for the system.What is the effect of the box in implicit solvent simulations? This is the mdp file that I am using: --run.mdp-

Re: [gmx-users] Box in Implicit Solvent Simulations

On 22/11/2011 10:08 PM, ifat shub wrote: Hi, I am running simulations using implicit solvent. I am using the pbc = no option in my mdp file, however, I see it the .gro file that gromacs is creating a box for the system.What is the effect of the box in implicit solvent simulations? None, if p

[gmx-users] Rv: g_helixorient question

Hi, I'm sorry to insist in my question but if somebody could answer or just to send me some information or place to look for, I will be very thanked. GROMACS manual does not give any information but the way to use it. Nothing about the contain of files. Thanks again.  - Mensaje reenviado -

Re: [gmx-users] Rv: g_helixorient question

On 22/11/2011 10:41 PM, Javier Romero Garcia wrote: Hi, I'm sorry to insist in my question but if somebody could answer or just to send me some information or place to look for, I will be very thanked. I imagine that these kinds of definitions are discussed in general texts on (computational

[gmx-users] Regarding Dimer calculations

Dear all, Could anybody suggest me how to do dimer calculation using gromacs or guide me to some paper or journal that describes the same. Thank you *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- gmx-users mailing listgmx-users@grom

Re: [gmx-users] Regarding Dimer calculations

On 22/11/2011 11:06 PM, Ravi Kumar Venkatraman wrote: Dear all, Could anybody suggest me how to do dimer calculation using gromacs or guide me to some paper or journal that describes the same. The same considerations apply - simulation design depends on what you wish to observe. F

Re: [gmx-users] do_dssp segmentation fault

Dear Alex, On Nov 22, 2011, at 9:28 AM, Alex Jemulin wrote: > Dear all > I'm experiencing the following error in Gromacs 4.5 with do_dssp > > Here is the command > do_dssp -f md.xtc -s md.tpr -o secondary-structure.xpm -sc > secondary-structure.xvg -dt 10 > > give me the following error > se

[gmx-users] Cavity detection on membrane protein surface

Dear all, I'm studying a membrane protein. During MD some concavities appear and disappear on its surface. I'd like to isolate atoms and residues involved in these formations. Any suggestion? Which steps should I follow to automate the identification process?   Thanks in adavance-- gmx-users mai

Re: [gmx-users] Cavity detection on membrane protein surface

On 23/11/2011 12:33 AM, Alex Jemulin wrote: Dear all, I'm studying a membrane protein. During MD some concavities appear and disappear on its surface. I'd like to isolate atoms and residues involved in these formations. Any suggestion? Which steps should I follow to automate the identification

[gmx-users] -ter flag, pdb2gmx

Dear gmx-users, I'm having some problems using the flag "-ter" of pdb2gmx. The syntax I'm using is the following, for a protein dimer: pdb2gmx -f protein_dimer.pdb -o start.gro -p start.top -ter Instead of prompting a menu with the choice of different c

[gmx-users] how to obtain NOEs from MD trajectory ?

Dear Gromacs users, Is there any algorithm/procedure to calculate NOEs from an MD trajectory? I'd greatly appreciate any references where the algorithm is described. Best regards, Jose M. Borreguero -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-

Re: [gmx-users] 2. Re: GROMACS/ORCA QMMM (Jose Tusell)

When GROMACS takes care of the optimization this doesn't happen. Jose R Tusell On Tue, Nov 22, 2011 at 12:35 AM, Gerrit Groenhof wrote: >  On 11/22/2011 04:02 AM, gmx-users-requ...@gromacs.org wrote: >> >>        gmx-users@gromacs.org >> >> To subscribe or unsubscribe via the World Wide Web, vi

Re: [gmx-users] 2. Re: GROMACS/ORCA QMMM (Jose Tusell)

Dear Jose, Also our calculations using bOpt with ORCA are fine. ORCA does not give the coordinates in nm, but in Angstrom. Which version of gromacs are you using? Christoph On 11/22/2011 03:53 PM, Jose Tusell wrote: When GROMACS takes care of the optimization this doesn't happen. Jose R Tusell

[gmx-users] Charged tube

Dear Gmx Users, I am wondering whether you know any software which allows to build a charged tube with specified dimensions which will work with Gromacs? Is it possible to add charges or e.g. add ions and use position restrained dynamics? Thank you, Steven -- gmx-users mailing listgmx-users

[gmx-users] pyroglutamate in gromos53a6

Dear all, Where can I find gromos53a6.ff parameters for pyroglutamate (PCA/ PGLU/ PGA) ? Alternatively, given that I have them in amber99.ff and oplsaa.ff is there a way I could adapt these to gromos53a6.ff? Can I use, for example, the gromos53a6.ff atom types from glutamine, add/remove

[gmx-users] SASA query

Hi Gromacs Users I have a query regarding g_sas which i intend to use for my MM/PBSA calcualtion i am planing to use g_sas for calculating the SASA using a probe radius of 0.14 nm is this okay ? o secondly ∆Gsolv,np = 0.00542*SASA + 0.92 is this master equation right third and important (1)

Re: [gmx-users] pyroglutamate in gromos53a6

Hi Henry, That would be a bit of a wild west approach. A better approximation would be taking the charges from the backbone amide group, as it is just an amide with on either side aliphatic carbons. Doing it properly is a bit more involved, as for the G53a6 FF you need to choose parameters giving

Re: [gmx-users] how to obtain NOEs from MD trajectory ?

Hi Jose, Check g_rmsdist -h Not sure about the references though. Cheers, Tsjerk On Nov 22, 2011 3:23 PM, "Jose Borreguero" wrote: Dear Gromacs users, Is there any algorithm/procedure to calculate NOEs from an MD trajectory? I'd greatly appreciate any references where the algorithm is descri

[gmx-users] pdb2gmx disulfide bond formation - missing bond, angle, & dihedral types with all GROMOS FFs

Greetings Gromacs Users, I am building the topology file for a protein with three disulfide bonds (bovine pancreatic trpysin inhibitor). When using any of the GROMOS FFs the topol.top output of pdb2gmx has missing bond, angle, and dihedral types on the lines describing the three disulfides. (Th

[gmx-users] Folding of small globular peptide

Dear Gromacs Users! I want to simulate folding of small globular protein in water. I have linear structure ( with all psi\ phi torsions set to 180 ) of my peptide made in HyperChem as well as NMR structure ( for control ). Could you tell me what specificities of such simmulation should I take i

Re: [gmx-users] pdb2gmx disulfide bond formation - missing bond, angle, & dihedral types with all GROMOS FFs

Hi Elizabeth, These missing terms are filled in automatically by grompp from the bondtypes, angletypes and dihedraltypes definitions in the *bon.itp. Unless grompp complains about missing terms, you'll be fine. You can check whether everything is okay by writing out a processed topology (grompp -p