[gmx-users] Water-Mediated Hydrogen Bonds

Dear All, I’m doing research in the field of Protein-DNA interaction. I have gone through these papers, *A “Solvated Rotamer” Approach to Modeling Water-Mediated Hydrogen Bonds at Protein–Protein Interfaces* *“Effect on DNA relaxation of the single Thr718Ala mutation in human topoisomerase I:

Re: [gmx-users] N-terminus problem

On 1/07/2011 8:35 PM, Emine Deniz Tekin wrote: Hi Gromacs users, I created a lipopeptide (lauroic acid connected to an 8-residue peptide which starts with Valine). How is the link from acid to peptide created? ·If I try to use pdb2gmx with -ter flag(Start terminus VAL-2: None, End termi

Re: [gmx-users] energygrps long-range interaction

Please make sure to keep the discussion on the gmx-users list. gyorgy.han...@fc.up.pt wrote: Thank you very much for the reply. So I guess the same holds for all Ewald-like long-corrections, right? Sounds right. But we don't have this problem with reaction field correction do we? Presum

Re: [gmx-users] how is dVpot/dlambda calculated

Dennis Sprous, PhD wrote: Could someone forward the citation of how dVpot/dlambda is calculated for a free energy run. I am specifically interested in knowing if it is an analytic or numeric based calculation. The equations relevant to free energy calculations are discussed in the manual

[gmx-users] how is dVpot/dlambda calculated

Could someone forward the citation of how dVpot/dlambda is calculated for a free energy run. I am specifically interested in knowing if it is an analytic or numeric based calculation. -- any problemworth attack proves its worth by fighting back Dennis Sprous, PhD BioLeap Inc. Cambr

Re: [gmx-users] interaction energy

balaji nagarajan wrote: Dear users ! thanks for the reply I was able to do that , otherwise we can select the number of the option one by one and enter then after that if we leave a empty line and enter it gives all the needed energy terms ! my intension is not to do like this is it

RE: [gmx-users] interaction energy

Dear users ! thanks for the reply I was able to do that , otherwise we can select the number of the option one by one and enter then after that if we leave a empty line and enter it gives all the needed energy terms ! my intension is not to do like this is it possible to give it alo

Re: [gmx-users] interaction energy

balaji nagarajan wrote: Dear Users ! i would like to do this to a set of files ! so how to print the required values in the text mode or is there any flag for this in I quoted the help description for how to do this. Is there some problem? For instance, if you want to write the potent

RE: [gmx-users] interaction energy

Dear Users ! i would like to do this to a set of files ! so how to print the required values in the text mode or is there any flag for this in g_energy , thanks in advance > Date: Fri, 1 Jul 2011 13:40:28 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-us

Re: [gmx-users] interaction energy

balaji nagarajan wrote: Dear Users ! Now i am able to do the protein solvent interaction ! thanks ! i have understood ! when i used the energygrps , when i used the g_energy -f em.edr this command it prints all terms and asks to make selection as below, 1 Bond 2 Angle

[gmx-users] interaction energy

Dear Users ! Now i am able to do the protein solvent interaction ! thanks ! i have understood ! when i used the energygrps , when i used the g_energy -f em.edr this command it prints all terms and asks to make selection as below, 1 Bond 2 Angle3 Proper-Dih.

Re: [gmx-users] energygrps long-range interaction

gyorgy.han...@fc.up.pt wrote: Dear Users, I'm wondering if it is possible to extract the long-range part of the interactions of energy-groups. In the output I see only short-range terms. I am interested in the total interaction energy of an energy group. I would guess that one should be a

[gmx-users] energygrps long-range interaction

Dear Users, I'm wondering if it is possible to extract the long-range part of the interactions of energy-groups. In the output I see only short-range terms. I am interested in the total interaction energy of an energy group. I would guess that one should be able to get the long-range par

Re: [gmx-users] micelle clustering

Hi Sulatha, With my clustering algorithm there can be no infinite loop :) By the way, sorry for the error messages you ran into with compiling 4.0.7. It had escaped me that these changes were made after that version. Cheers, Tsjerk On Fri, Jul 1, 2011 at 8:29 AM, sulatha M. S wrote: > Thanks M

Re: [gmx-users] solvent_protein interaction energy

balaji nagarajan wrote: Thanks for the reply ! I have tried building the topology with generating the index file make_ndx -f * it gave options i have selected the protein and the solvent An index file is unnecessary for default groups. http://www.gromacs.org/Documentation/Terminolo

Re: [gmx-users] 3rd neighbor

Otto Master wrote: Hi Everyone, I would like to do some changes to the non bonded parameter of GROMOS force field. Especially, I like modify the 3rd neighbor parameters. Unfortunately, I cannot find them in the ffnonbonded.itp file. I assume that the parameter in [ atomtypes ] block are take

[gmx-users] solvent_protein interaction energy

Thanks for the reply ! I have tried building the topology with generating the index file make_ndx -f * it gave options i have selected the protein and the solvent then i gave minimization in the minimization file i have included energygrps = Protein SOL , but the energy file ha

[gmx-users] g_velacc

Hello, I am trying to calculate the velocity autocorrelation function for my system. I have a system with glucose + ionic liquids (128 emi (cations) and 128 Cl (anions)). I am not getting proper velocity autocorrelation function. g_velacc -f 6.trr -s 6.tpr -n glu-emi-cl-128-no.ndx -nonormalize

[gmx-users] N-terminus problem

Hi Gromacs users, I created a lipopeptide (lauroic acid connected to an 8-residue peptide which starts with Valine). · If I try to use pdb2gmx with -ter flag (Start terminus VAL-2: None, End terminus ASP-9: COO-), everything seems to work (topology is created.). · But, if I t

Re: [gmx-users] Installation of gromacs-gpu on windows

Thank you for your reply! Now can I have your attention for another quetsion? I'm not very experienced in Visual Studio because I do almost all of my work under linux. But now it is necessary to compile gromacs-gpu under windows. Could someone point me to a tutorial or how-to about step-by-step com

[gmx-users] 3rd neighbor

Hi Everyone, I would like to do some changes to the non bonded parameter of GROMOS force field. Especially, I like modify the 3rd neighbor parameters. Unfortunately, I cannot find them in the ffnonbonded.itp file. I assume that the parameter in [ atomtypes ] block are taken from Table 7 (Oostenbrin

Re: [gmx-users] PME energy calculation

On 1/07/2011 5:51 PM, 李浩 wrote: > > Hello Everyone, > > I am using PME(4.05) to calculate the long-rang electrostatic > interaction, but when I finished the > > Simulation, I found that I can’t get the result of energy of the part > of “fourier space（long range part）”. In other word，there is only a

Re: [gmx-users] Energy-groups?

You can specify the energygrps in mdp file, grompp a new tpr file and use -rerun option of the mdrun to get a new edr file Cheers Jianguo From: "nishap.pa...@utoronto.ca" To: gmx-users@gromacs.org Sent: Tuesday, 7 December 2010 02:56:04 Subject: [gmx-user

[gmx-users] PME energy calculation

Hello Everyone, I am using PME(4.05) to calculate the long-rang electrostatic interaction, but when I finished the Simulation, I found that I can’t get the result of energy of the part of “fourier space（long range part）”. In other word，there is only a congregation of energy of that named Coul. re

Re: [gmx-users] energy_extract

On 1/07/2011 4:40 PM, balaji nagarajan wrote: Dear Users ! I have took a penta peptide and did topology generation , I have solvated it with water box , now i did a minimization with zero step , to know the energy of the initial molecule , i used g_energy for the out put , like $ g_energy