[gmx-users] Nose-hoover T-coupling in REMD

Dear all, I posted yesterday but didn't get answer..I guess it's due to my wrong approach to ask. I would like to explain more and hope I would get your help. I'm doing an REMD, and want to have a strong temperature coupling to make sure every replica is at its target temperature. I guess I could

Re: [gmx-users] buckingham potentials

sreelakshmi ramesh wrote: Dear justin, I have no clues about rewriting a force field so i think i can t proceed with this anymore. thanks a lot for your patient reply. For the future, you will waste a lot less time (your own, and that of those who are trying to help yo

Re: [gmx-users] buckingham potentials

Dear justin, I have no clues about rewriting a force field so i think i can t proceed with this anymore. thanks a lot for your patient reply. sree. On Wed, Dec 22, 2010 at 9:32 AM, Justin A. Lemkul wrote: > > > sreelakshmi ramesh wrote: > >> Dear justin, >>

Re: [gmx-users] buckingham potentials

sreelakshmi ramesh wrote: Do u mean to say that all the force fields available in gromacs are default to be used only for LJ potential. Yes. That's why they all have their [defaults] directives set to use LJ. -Justin On Wed, Dec 22, 2010 at 9:32 AM, Justin A. Lemkul

Re: [gmx-users] buckingham potentials

Do u mean to say that all the force fields available in gromacs are default to be used only for LJ potential. On Wed, Dec 22, 2010 at 9:32 AM, Justin A. Lemkul wrote: > > > sreelakshmi ramesh wrote: > >> Dear justin, >> I am sorry the file is ffG43a1nb.itp.It < >> http://ffG43a1n

Re: [gmx-users] buckingham potentials

sreelakshmi ramesh wrote: Dear justin, I am sorry the file is ffG43a1nb.itp.It was a typing mistake. The points I raised before still stand: 1. You're not using 43A1, you're using ffgmx, according to that message from grompp. 2. You can't make

Re: [gmx-users] buckingham potentials

Dear justin, I am sorry the file is ffG43a1nb.itp.It was a typing mistake. On Wed, Dec 22, 2010 at 9:26 AM, Justin A. Lemkul wrote: > > > Justin A. Lemkul wrote: > >> >> >> sreelakshmi ramesh wrote: >> >>> I am using gromos force field fotr my work and This force field's files >

Re: [gmx-users] buckingham potentials

Justin A. Lemkul wrote: sreelakshmi ramesh wrote: I am using gromos force field fotr my work and This force field's files come filled with LJ functions and now if i want to work with buckingham potential i changed in default section of force field ffG34a21.itp file but it gives me the fo

Re: [gmx-users] buckingham potentials

sreelakshmi ramesh wrote: I am using gromos force field fotr my work and This force field's files come filled with LJ functions and now if i want to work with buckingham potential i changed in default section of force field ffG34a21.itp file but it gives me the follwing errors ERROR 77 [

Re: [gmx-users] buckingham potentials

I am using gromos force field fotr my work and This force field's files come filled with LJ functions and now if i want to work with buckingham potential i changed in default section of force field ffG34a21.itp file but it gives me the follwing errors ERROR 77 [file ffgmxnb.itp, line 144]: Try

Re: [gmx-users] compilation instructions, the gromacs wiki, documentation, and test suites

chris.ne...@utoronto.ca wrote: Dear Roland: I am not sure what my barrier is electronically, only that there is a barrier. The web site has changed since my last attempt to make modifications, but I still can not add to the site as I once could when it was simply a wiki. Currently, I have a

[gmx-users] compilation instructions, the gromacs wiki, documentation, and test suites

Dear Roland: I am not sure what my barrier is electronically, only that there is a barrier. The web site has changed since my last attempt to make modifications, but I still can not add to the site as I once could when it was simply a wiki. Currently, I have a tab labeled "[MISSING: skin.

Re: [gmx-users] buckingham potentials

sreelakshmi ramesh wrote: so if i set vdwtype =cut off and specify 2 in default section (2 is for buck and 1 for LJ ) of topology file will gromacs makes suer that i want the calculation with bucking ham potential. Presumably, since that's what the manual would indicate works. You can ans

Re: [gmx-users] buckingham potentials

so if i set vdwtype =cut off and specify 2 in default section (2 is for buck and 1 for LJ ) of topology file will gromacs makes suer that i want the calculation with bucking ham potential. On Wed, Dec 22, 2010 at 8:32 AM, Justin A. Lemkul wrote: > > > sreelakshmi ramesh wrote: > >> Thanks a lot f

Re: [gmx-users] buckingham potentials

sreelakshmi ramesh wrote: Thanks a lot for timely reply by gmxusers.I read the manual and i had altered the buckingham coefficients in topolgy file.Now in mdp file in vdwtype i want to specify it as buckingham but looks like i can mention only LJ and in manual they haven't told about the nota

Re: [gmx-users] buckingham potentials

Thanks a lot for timely reply by gmxusers.I read the manual and i had altered the buckingham coefficients in topolgy file.Now in mdp file in vdwtype i want to specify it as buckingham but looks like i can mention only LJ and in manual they haven't told about the notation for BJ.any suggestions plea

Re: [gmx-users] Re: gb_saltconc in implicit water simulations

Hi Per (and all), I am trying to recreate the results of the CHARMM forcefield implementation to better understand how to implement implicit solvent models, but I can't quite recreate your results. If the Gromacs code doesn't use salt concentrations, does that mean that your simulations

Re: [gmx-users] Re:Crash error

lloyd riggs wrote: Dear All, I had posted part of the error below. I still have not the problem solved, everything from gromacs runs, including short energy minimizations, but if I run an MD I get the log ending; Started mdrun on node 0 Thu Dec 9 16:56:10 2010 Step T

[gmx-users] Re:Crash error

Dear All, I had posted part of the error below. I still have not the problem solved, everything from gromacs runs, including short energy minimizations, but if I run an MD I get the log ending; Started mdrun on node 0 Thu Dec 9 16:56:10 2010 Step Time Lambda

Re: [gmx-users] Umbrella sampling

Nilesh Dhumal wrote: Hello I am trying to run umbrella sampling for my system. I have system with four ion pairs (4 cation and 4 anion) of ionic liquids and 1024 water molecules. I am trying to PMF calculation with cation-anion distance as a reaction coordinate. I choose cation as group1 and a

[gmx-users] Umbrella sampling

Hello I am trying to run umbrella sampling for my system. I have system with four ion pairs (4 cation and 4 anion) of ionic liquids and 1024 water molecules. I am trying to PMF calculation with cation-anion distance as a reaction coordinate. I choose cation as group1 and anion group2. I am getting

Re: [gmx-users] fac value for distance or h-bonding restraints

udaya kiran wrote: Dear GROMACS users, I am working on a cyclic peptide dynamics in DMSO solvent box with ffG53a6 force filed. As the results are not satisfactory, I have carried out the MD by restraining couple of hydrogen bonds. However, the results are same as unrestrained calculations

[gmx-users] fac value for distance or h-bonding restraints

Dear GROMACS users, I am working on a cyclic peptide dynamics in DMSO solvent box with ffG53a6 force filed. As the results are not satisfactory, I have carried out the MD by restraining couple of hydrogen bonds. However, the results are same as unrestrained calculations when I used the "fac" val

Re: [gmx-users] g-dist

mohsen ramezanpour wrote: Dear Justin WARNING 1 [file g-dist.mdp, line unknown]: Can only use nstype=Simple with pbc=no, setting nstype to Simple WARNING 2 [file complex.top, line 39718]: Bad box in file complex.gro Generated a cubic box 10.816 x 14.959 x9.086 Warning: atom name 6

Re: [gmx-users] g-dist

Dear Justin WARNING 1 [file g-dist.mdp, line unknown]: Can only use nstype=Simple with pbc=no, setting nstype to Simple WARNING 2 [file complex.top, line 39718]: Bad box in file complex.gro Generated a cubic box 10.816 x 14.959 x9.086 Warning: atom name 6439 in complex.top and complex

Re: [gmx-users] g-dist

mohsen ramezanpour wrote: Dear justin after using grompp without -maxwarn I faced these: NOTE 2 [file g-dist.mdp, line unknown]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 2 Mb

Re: [gmx-users] g-dist

Dear justin after using grompp without -maxwarn I faced these: NOTE 2 [file g-dist.mdp, line unknown]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. This run will generate roughly 2 Mb of data writing run input file

Re: [gmx-users] g-dist

mohsen ramezanpour wrote: Dear All I did the Enzyme/drug tutorial and generated complex.gro and complex.top files as was said. Now I want to measure the distance between center of mass of protein and drug I used g_dist but I could not. I entered these commands(of course I made an index.ndx a

[gmx-users] g-dist

Dear All I did the Enzyme/drug tutorial and generated complex.gro and complex.top files as was said. Now I want to measure the distance between center of mass of protein and drug I used g_dist but I could not. I entered these commands(of course I made an index.ndx and g-dist.tpr): I used from an t

[gmx-users] Nose-hoover T-coupling nsttcouple

Dear all, I wonder what will happen in Nose-hoover coupling when tau_t = dt * nsttcouple, while nsttcouple = nstlist. (I used -maxwarn 1 to ignore the Gromacs warning) I tried this setting, to find the temperature is OK, but I am not sure whether it will introduce some artifacts in the simulation

Re: [gmx-users] buckingham potentials

sreelakshmi ramesh wrote: can anyone tell me how to alter the parameter B OF buckingham potential. Manual, chapter 5, especially table 5.4, which specifically lists all of the parameters and where they are defined. -Justin regards, sree -- Ju

Re: [gmx-users] reagrding huggins meyer potential

sreelakshmi ramesh wrote: Dear all, I wanted to simulate Nacl in water using huggins meyer potential as vdw type.since gromacs has just LJ OR BJ potential i wanted to know if somebody had done it with huggins meyer potential.I read the manual and since i am not good in c or fort

[gmx-users] buckingham potentials

can anyone tell me how to alter the parameter B OF buckingham potential. regards, sree -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please do

[gmx-users] free energy of methan disappearing:tutorial

Dear All I want to calculate protein-drug binding free energy. I read Dr.Mobley tutorial(about free energy of methan dissapearing from water).I couldn't understand some of it's parts. Can I use thisr tutorial in this case(protein-drug)? Besides, I have a few question about that: 1-What do I nee