Re: [gmx-users] Re: generating a top file

Yang Ye wrote: Hi, Saf We use a special bond for heme, specified in specbond.dat. Check the mailing list archive. Or http://wiki.gromacs.org/index.php/specbond.dat Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mail

Re: [gmx-users] generating a top file

Shahrokh Safarian wrote: Dear colleagues As you know if we want to introduce a new molecule into Gromacs, the related parameters for that molecule (e.g. [atoms], [bonds], [pairs], [dihedrals] and so on) should be inserted to the Gromacs rtp file. Strictly, no. Only if you want pdb2gmx to recog

Re: [gmx-users] Fwd: Individual energies of amino acids

abhigna polavarapu wrote: Hi Mark, I need to calculate the individual energies of aminoacids using Gromacs. But while using energygrps option in .mdp file for each amino acid I can only calculated the nonbonded energies of this residue. Is there a way where I can calculated th

Re: [gmx-users] adding counter ions

OZGE ENGIN wrote: Hi all, My peptide contains two adversely charged residues. I use PME option for the investigation of electrostatic interactions within my system. The total charge of the box must be neutral. Since the system contains adversely charged residues, is it still necessary to add

Re: Re: [gmx-users] OT: script to mutate residues

You may try NOC, downloading at http://noch.sourceforge.net It can do residue by residue mutation in GUI. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.grom

Re: [gmx-users] flexible molecular alignment

I've coded a model for real time structure alignment in NOC http://noch.sourceforge.net It's easy to adapt the code to fit your need. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the

Re: [gmx-users] dPCA "atoms"

Thanks Yang Ye! I will look into this further. Thanks for the program, I'm sure that will save me much time. Russell Green On 6/11/07, Yang Ye <[EMAIL PROTECTED]> wrote: As what we normally do with dPCA, after obtaining the 2D projection of first and second principle, we make it into a 3D pl

Re: [gmx-users] dPCA "atoms"

Yang Ye wrote: As what we normally do with dPCA, after obtaining the 2D projection of first and second principle, we make it into a 3D plot of free energy surface. The awk program is provided below to do such conversion. On this surface, we can located regions with low free energy and this lead

Re: [gmx-users] dPCA "atoms"

As what we normally do with dPCA, after obtaining the 2D projection of first and second principle, we make it into a 3D plot of free energy surface. The awk program is provided below to do such conversion. On this surface, we can located regions with low free energy and this leads us to go back

Re: [gmx-users] genion - why shall we neutralize the charges?

Hi, First, our simulation system in physical world are mostly neutralized instead of carrying charges. Second, there is requirement for PME for electrostatic calculations. Neutralization is a not a must in 3.3.1 Gromacs; a background charge will complement for the charges that system carries, b

Re: [gmx-users] trjconv -drop drop.xvg ??

-dropunder -dropover - Original Message From: "[EMAIL PROTECTED]" <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Tuesday, June 12, 2007 1:57:25 AM Subject: [gmx-users] trjconv -drop drop.xvg ?? Dear community, Could anybody help me out with the -drop option of trjconv? I would like

[gmx-users] dPCA "atoms"

Dear Gromacs community, I've been using the PCA analysis in dihedral space for a chain of my protein of interest. I made a script to collect the atom quadruplets corresponding to the phi and psi angles and output them to an index file. I followed the steps in the paper manual and everything w

[gmx-users] trjconv -drop drop.xvg ??

Dear community, Could anybody help me out with the -drop option of trjconv? I would like to have trjconv re-write an xtc trajectory dropping frames of given time values that I inserted into a file called "drop.xvg". This file looks like: 1 4.5 etc. (one single column with times (ps) of the frame

Re: [gmx-users] genion

Elias santos wrote: Hi!! I want know because we must neutralize the total load of the system (protein + water) into of the box with genion. You should neutralize the system and you also may want to add extra ions to get up to physiological salt concentration. --

[gmx-users] genion

Hi!! I want know because we must neutralize the total load of the system (protein + water) into of the box with genion. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at htt

[gmx-users] flexible molecular alignment

Hi there, I know this is not related to GMX but was wondering if you could kindly help me out to find a program for flexible alignment of molecules. I know GASP from Tripos but will appreciate it if you could introduce to me others programs available out there either commercial or freewares. B

[gmx-users] g_mindist -pi option

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 that the box is larger enough. After 6ns I get this result: 0

[gmx-users] Re:Regarding mdrun sigmentation fault in cluster

Dear David and Stephan, Thank you for your suggestion and I will go through it. If i will get any problem, I contact you. with regards, Ngaraju Mulpuri.

Re: [gmx-users] tpbconv restart crashing on 3.3.1

yes, tpbconv has been given the energy file. gmxcheck says trr and edr files look happy, the original .tpr looks fine from gmxdump and doesn't crash when it's rerun, and any output from tpbconv looks fine from scanning bits of it in text format, though it's a pretty massive file and I've no ide