[gmx-users] Re: gmx-users Digest, Vol 93, Issue 72

Dear All, Could anybody tell me how to take the coordinates of the first and second solvation shell with solute from the snapshots of MDS run. Which molecular viewer will be good for it. Thank you *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-96869339

[gmx-users] Regarding Molecular Viewer

Dear All, > Could anybody tell me how to take the coordinates of the > first and second solvation shell with solute from the snapshots of MDS run. > Which molecular viewer will be good for it. > > Thank you > > *With Regards, > Ravi Kumar Venkatraman, > IPC Dept., IISc, > Bangalore, IN

[gmx-users] constrained mdrun about linear rigid molecule ??

Hi, I'm not good at handling Gromacs yet. My question is about virtual interaction. I'm doing simulation dealing with CO2 which is linear rigid molecule as you already know. As pervasively known, I introduced virtual sites. However, I don't know how to give initial coordinate correctly of dummy

[gmx-users] Protein angles / single point calculations

Hi, I have some questions. First, what dihedral angles will Gromacs produce and use in topology when simulating proteins? To be more specific, I was looking for psi (N-C(a)-C-N) and phi (C-N-C(a)-C) angles in all the dihedrals that were generated by pdb2gmx. I only found the psi angles but not

Re: [gmx-users] Protein angles / single point calculations

On 12/01/2012 9:14 PM, Matthias Ernst wrote: Hi, I have some questions. First, what dihedral angles will Gromacs produce and use in topology when simulating proteins? To be more specific, I was looking for psi (N-C(a)-C-N) and phi (C-N-C(a)-C) angles in all the dihedrals that were generated b

Re: [gmx-users] PRODRG charges

Hi Many thanks for your reply and sorry to come back on this. Is the fitting to experimental free energies of solvation, the only acceptable way to get "GROMOS-compatible charges"? Acceptable because this is the way that partial charges were derived for the gromos ff. In the quite usual case tha

Re: [gmx-users] PRODRG charges

On 2012-01-12 12:42, g...@bioacademy.gr wrote: Hi Many thanks for your reply and sorry to come back on this. Is the fitting to experimental free energies of solvation, the only acceptable way to get "GROMOS-compatible charges"? Acceptable because this is the way that partial charges were derive

Re: [gmx-users] PRODRG charges

On 12/01/2012 10:42 PM, g...@bioacademy.gr wrote: Hi Many thanks for your reply and sorry to come back on this. Is the fitting to experimental free energies of solvation, the only acceptable way to get "GROMOS-compatible charges"? Acceptable because this is the way that partial charges were der

Re: [gmx-users] Problem with FE-Cys covalent bond

Hi: Did you add the parameters for the new covalent bond to the correct part of ffbonded.itp? Because, for the GROMOS FF you have to add the parameters for the new bond, angle and dihedral ,created due to specbond, in a certain part of the ffbonded.itp for pdb2gmx be able to use it. I dont know if

[gmx-users] problem with gromacs

Hello, Thanks for your advice. I use "make distclean" before configure. But an error appeared in the same place. cd gromacs-4.5.5 make distclean ./configure --disable-threads make .libs/xlate.o:xlate.c:(.text+0xa9b): undefined reference to `_put_symtab' .libs/xlate.o:xlate.c:(.text+0xb3a): u

Re: [gmx-users] constrained mdrun about linear rigid molecule ??

On 12/01/2012 8:40 PM, Kiwoong Kim wrote: Hi, I'm not good at handling Gromacs yet. My question is about virtual interaction. I'm doing simulation dealing with CO2 which is linear rigid molecule as you already know. As pervasively known, I introduced virtual sites. However, I don't know how

[gmx-users] Pull code problem: Large fluctuations in pull force in Gromacs 4.5.1 compared to 4.0.5

Dear all, I have a problem using the pull code in Gromacs 4.5.1. I am running simulations with a small molecule at constrained distances from the bilayer center in a membrane (z-direction) in order to calculate permeability data. I use the force acting on the molecule (pullf.xvg) at different di

[gmx-users] optimum acceptance ratio for REMD

Hi all, I am currently puzzled by the emphasis on using an acceptance ratio of around 0.2 for replica exchange simulations in the literature. This optimum ratio is, as far as I understand, derived assuming that the exchange attempt frequency is constant and that the protein dynamics are not limit

Re: [gmx-users] optimum acceptance ratio for REMD

On 2012-01-12 19:42, Ben Reynwar wrote: Hi all, I am currently puzzled by the emphasis on using an acceptance ratio of around 0.2 for replica exchange simulations in the literature. This is bogus indeed. You are correct. Many people prefer not to think. What matters is that the time between

[gmx-users] Graphene - force field

Hello, I am trying to run simulation of graphene oxide. I have 16 carbon atoms of same type. I am using opls force field. could make the .itp file and pasted here [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1 3 yes 0.5

[gmx-users] difference in Coulomb SR and Coulomb 14?

Dear experts, Can you please make me understand the actual difference between Coulomb SR and Coulomb 14? -- Saba Ferdous Research Scholar (M. Phil) National Center for Bioinformatics Quaid-e-Azam University, Islamabad Pakistan -- gmx-users mailing listgmx-users@gromacs.org http://lists.grom

Re: [gmx-users] difference in Coulomb SR and Coulomb 14?

On 13/01/2012 4:41 PM, Saba Ferdous wrote: Dear experts, Can you please make me understand the actual difference between Coulomb SR and Coulomb 14? See manual 3.4.7 for short-range interactions and 4.6.1 for 1-4. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.o

Re: [gmx-users] Graphene - force field

On 13/01/2012 2:22 PM, Nilesh Dhumal wrote: Hello, I am trying to run simulation of graphene oxide. I have 16 carbon atoms of same type. I am using opls force field. could make the .itp file and pasted here [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ ;1