Re: [gmx-users] Using Charmm FF with implicit solvent on gromacs

On 19/11/2010 8:49 AM, César Ávila wrote: Dear all, I would like to know if anyone has experience on running simulations using the Charmm FF and implicit solvent model on gromacs. I have found that gromacs has three implementations for GB models * Still * Hawkins-Cramer-Truhlar (HCT)

Re: [gmx-users] 4-site rigid body model

Sanku M wrote: Hi, I have a molecule consisting of 4 sites which have fixed relative positions interacting only through LJ and coulomb interaction. I was wondering how can I do MD simulation in GROMACS keeping the geometry unchanged . Is just putting constraints along all the possible

Re: [gmx-users] Area per lipid calculation

NG HUI WEN wrote: Dear gromacs users, I have a protein embedded in a lipid bilayer. After sufficient equilibration of the system ( i.e. size of box X and Box Y became quite constant), I would now like to assess the area per lipid of my system. However, (I think) I could not simply do

[gmx-users] 4-site rigid body model

Hi, I have a molecule consisting of 4 sites which have fixed relative positions interacting only through LJ and coulomb interaction. I was wondering how can I do MD simulation in GROMACS keeping the geometry unchanged . Is just putting constraints along all the possible distances and usi

[gmx-users] Area per lipid calculation

Dear gromacs users, I have a protein embedded in a lipid bilayer. After sufficient equilibration of the system ( i.e. size of box X and Box Y became quite constant), I would now like to assess the area per lipid of my system. However, (I think) I could not simply do this ( average size o

[gmx-users] Cumulative coordination number?

Dear all, I am trying to calculate the cumulative coordination number of solvents around my solute as a function of distance but the result obtained seem not reasonable. I used the following command. g_rdf -f DD.xtc -s DD.gro -n DD.ndx -cn -b 18000 -e 2-o CNDD.xvg My solvent molecule

[gmx-users] Using Charmm FF with implicit solvent on gromacs

Dear all, I would like to know if anyone has experience on running simulations using the Charmm FF and implicit solvent model on gromacs. I have found that gromacs has three implementations for GB models - Still - Hawkins-Cramer-Truhlar (HCT) - Onufriev-Bashford-Case (OBC) The charmm FF

[gmx-users] genion writes a log file?

Hi, When using versions 4.5.2 and 4.5.3, I have noticed that genion now outputs a file called "genion.log" (or "genion_node0.log" with 4.5.2) that appears to contain the header information normally found in an md.log file produced by mdrun (see below). Is this normal? There really isn't any

Re: [gmx-users] Gromacs "Quotes"

On 2010-11-18 20.48, Sikandar Mashayak wrote: Hi I am wondering where can I find the file containing all the Gromacs Quotes , which are printed at the end of program run? thanks sikandar share/gromacs/top/gurgle.dat -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. B

[gmx-users] Gromacs "Quotes"

Hi I am wondering where can I find the file containing all the Gromacs Quotes , which are printed at the end of program run? thanks sikandar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org

Re: [gmx-users] cutoff values for amber ff

Jarmila Husby wrote: Dear all, I am setting-up a simulation of a protein-DNA complex using amber force field. In the manual (v4.5.3) I have found the recommended cutoff distances for electrostatics - coulombtype using PME (rcoulomb=rlist=rvdw = 0.9nm) with Gromos ff. However, I am aware

[gmx-users] cutoff values for amber ff

Dear all, I am setting-up a simulation of a protein-DNA complex using amber force field. In the manual (v4.5.3) I have found the recommended cutoff distances for electrostatics - coulombtype using PME (rcoulomb=rlist=rvdw = 0.9nm) with Gromos ff. However, I am aware the cutoff values are speci

Re: [gmx-users] Parameterization

You could use GLYCAM which is in AMBER so the parameters are already there in the correct format (but not in the AMBER ported to GROMACS) and convert that to GROMACS topology. It'll save you some time :) I had problems converting the improper dihedral that holds the NAc group planar using amb2gmx.p

Re: [gmx-users] DNA didnot wrap around CNT

Siamkhanthang Neihsial wrote: Hi friends, I have a DNA sequence (5'-GAG TCT GTG GAG GAG GTA GTC-3') and a CNT(6,5) of 90 Angstroms in length. I kept the DNA & CNT at a distance of 1 angstrom. Solvents molecules(water) inside CNT are removed at a radius of CNT at 4.2 . Equilibration

[gmx-users] DNA didnot wrap around CNT

Hi friends, I have a DNA sequence (5'-GAG TCT GTG GAG GAG GTA GTC-3') and a CNT(6,5) of 90 Angstroms in length. I kept the DNA & CNT at a distance of 1 angstrom. Solvents molecules(water) inside CNT are removed at a radius of CNT at 4.2 . Equilibration at 1000 steps, results in diminished

Re: [gmx-users] Reg: Unit Of Surface Tension

All output is in gromacs units, so it is bar*nm 1 bar*nm = 0.1 mN/m = 0.1 dyn/cm That is exactly what the two posts are explaining. Sven vinothkumar mohanakrishnan schrieb: > Hi all > > What is the unit of Surface tension that one obtains from Gromacs > using the g_energy command?. I searched the

Re: [gmx-users] detailed energies per interaction

On 18/11/2010 6:32 PM, Efrat Noy wrote: Hi, How can I get detailed energies per interaction (that is bonding and non-bonding terms for each pair/threesome/foursome of atoms) in Gromacs? Thanks, Efrat Please search the archives before posting. There have been several threads on this in the la

[gmx-users] detailed energies per interaction

Hi, How can I get detailed energies per interaction (that is bonding and non-bonding terms for each pair/threesome/foursome of atoms) in Gromacs? Thanks, Efrat-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at ht