[gmx-users] co-ordinate number mismatch

grep out each molecule type and pipe it to wc -l to find out how many atoms of each type you have in your .gro file, then compare this value to your .top file. This will help you identify which molecule is incorrectly represented in the .top file. e.g. # find number of SOL in the .gro grep SOL

[gmx-users] g_velacc

Hello, I am calculating the velocity auto-correlation function for my system which have 128 cation and 128 anion. How the program calculate the total velocity auto-correlation function? Does it average the velocity over all atoms at each time step? Thanks Nilesh -- gmx-users mailing list

Re: [gmx-users] Re: LINCS metal-ligand bonds

Thanks Justin & Chaban. Even I did the simulation for 3 ns and it worked well. Now the issue in my case is , while I was not imposing the M-N constraints, the metal was rattling around (little bit) and the histidine residues were moving back and forth (elongation of M-Nhis length). So I employed

[gmx-users] Re: Nucleotide terminal problems in GORMOS96 force field

Thank for your instant reply. I've copy the topology description into .rtp file, and update the residuetypes.dat file, pdb2gmx didn't show any message about residue recognition problem, so I think gromacs accepted my new residues. so, I think the only way is to add new terminal entry for nucleoti

Re: [gmx-users] Nucleotide terminal problems in GORMOS96 force field

On 10/12/12 2:03 PM, gatidaniel wrote: I am going to simulate a tRNA molecule using GROMOS96 force field, which contain some modified nucleotide. I've build the .rtp entry for each modified residues like the this: A02-mdf.top But

[gmx-users] Nucleotide terminal problems in GORMOS96 force field

I am going to simulate a tRNA molecule using GROMOS96 force field, which contain some modified nucleotide. I've build the .rtp entry for each modified residues like the this: A02-mdf.top But pdb2gmx prompt out such error message: F

Re: [gmx-users] Ignoring -of

On 10/12/12 1:41 PM, Amir Abbasi wrote: Hi Dear users! I have 28 dihedrals in my system. when I use g_angle to see evolution of average of these dihedrals during time using -of flag,I got this message: Warning: calculating fractions as defined in this program makes sense for Ryckaert Bellemans

[gmx-users] Ignoring -of

Hi Dear users! I have 28 dihedrals in my system. when I use g_angle to see evolution of average of these dihedrals during time using -of flag,I got this message: Warning: calculating fractions as defined in this program makes sense for Ryckaert Bellemans dihs. only. Ignoring -of g_angle reads tra

[gmx-users] Re: [gmx-developers] shell polarizable water model

Hi, please google for "polarization catastrophe". There is is a good review by Van Gunsteren on this issue. I am afraid there is not a simple solution for your problem. You may want to try the swm4-dp model, which was more stable in our simulations. Cheers, Jochen Am 10/11/12 8:36 PM, schri

Re: [gmx-users] Re: LINCS metal-ligand bonds

On 10/12/12 10:39 AM, Dr. Vitaly Chaban wrote: On 10/12/12 2:42 AM, tarak karmakar wrote: Dear ALL, In my protein I need to constraint the length between the Metal and the N of Histidine residues. In the .rtp file I didn't specify this Mn-N connectivity; these are more or less coordinate bo

Re: [gmx-users] Martini FF....

On 10/12/12 10:42 AM, rama david wrote: Hi Gromacs friends, I planed to use martini coarse grained ff to my simulation protocol. My simulation protocol is: I am placing two peptide at far distance.IAt these point i am using Gromos FF they are initially in random coil structure. Now when I r

[gmx-users] small tc-group

Use the sd integrator and specify System as the single temperature coupling group. integrator = sd tc_grps = System tau_t = 1.0 ld_seed = -1 If you're doing US simulations, then you're probably not going to be looking at dynamic information in any event so you lose nothing by doing velocity Lan

Re: [gmx-users] about salt concentration

@Christopher Neale The terminal part of the protein is folded in the starting conformation but disordered under natural conditions. In the 150 ns simulation, the terminal helices instead of unfolding, as the NMR experiments suggest, they turned upwards interacting with the rest of the protein, whi

Re: [gmx-users] LINCS metal-ligand bonds

On 10/12/12 2:42 AM, tarak karmakar wrote: Dear ALL, In my protein I need to constraint the length between the Metal and the N of Histidine residues. In the .rtp file I didn't specify this Mn-N connectivity; these are more or less coordinate bonds. So to do that I specified the Mn, N-atom in

Re: [gmx-users] delta G of binding for protein-ligand complex

On 10/12/12 5:44 AM, Archana Sonawani wrote: Dear Gromacs Users, I have two large organic compounds and one peptidomimetic binding to same receptor protein. I want to compare the delatG of binding of all the three complexes to show that peptidomimetic binds with greater affinity to protein. Ac

Re: [gmx-users] question about NVT run

On 10/12/12 9:39 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I want to do a md run for my membrane protein. For this I first did the energy minimization run. This finished with no errors. Here is the output of it: Steepest Descents did not converge to Fmax < 10 in 500

[gmx-users] question about NVT run

Hi everybody, I want to do a md run for my membrane protein. For this I first did the energy minimization run. This finished with no errors. Here is the output of it: Steepest Descents did not converge to Fmax < 10 in 5001 steps. Potential Energy = -8.7463000e+05 Maximum force = 4.5984982e+0

Re: [gmx-users] Re: small tc-group

On 2012-10-12 04:40:35AM -0700, fciocco wrote: > Thanks Peter for your reply > > actually, I did not think about that possibility because in the most > windows, I have this small highly charged peptide out of the membrane. > Moreover, in the last US windows, the peptide creates a defect and there

Re: [gmx-users] Lennard-Jones Parameters

On 10/12/12 8:04 AM, cuong nguyen wrote: Dear Gromacs Users, I got the .gro and .top files of 1-octanol downloaded from PRODRG website. Please let me know if I can change charge, epsilon and sigma of the molecule as written in a paper? and How to do? Atom types from PRODRG rarely, if ever

Re: [gmx-users] GBSA with ligands

Hi Alan, thank you for the reply. I have already read the previous related questions, but thanks for pointing that out anyways. I will develop my doubt further here. According to what I saw in the list I can simply borrow the parameters from the force field gbsa.itp in a chemical

Re: [gmx-users] GBSA with ligands

Hi, the issue is not with Antechamber or Acpype. There were similar questions to yours here (try searching GMX mail archives). The problem is you need to create the GBSA.itp parameters for you ligand. Which Acpype does is to create/convert Amber/GAFF parameters to usual MD in Gromacs. Alan On 12

[gmx-users] Re: small tc-group

Thanks Peter for your reply actually, I did not think about that possibility because in the most windows, I have this small highly charged peptide out of the membrane. Moreover, in the last US windows, the peptide creates a defect and there are several water molecules inside the membrane. So, if I

[gmx-users] delta G of binding for protein-ligand complex

Dear Gromacs Users, I have two large organic compounds and one peptidomimetic binding to same receptor protein. I want to compare the delatG of binding of all the three complexes to show that peptidomimetic binds with greater affinity to protein. According to the gromacs tutorial, I have to perfo

Re: [gmx-users] When are .trr files essential?

On 12/10/2012 6:27 PM, Jianguo Li wrote: One situation is the analysis that require velocities, such as calculating velocity autocorrelation function or lateral pressure. Or forces, for some reason. Also see http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume H

Re: [gmx-users] When are .trr files essential? (was: Regarding Gromacs output files)

One situation is the analysis that require velocities, such as calculating velocity autocorrelation function or lateral pressure.  -Jianguo From: Ladasky To: gmx-users@gromacs.org Sent: Friday, 12 October 2012, 13:25 Subject: [gmx-users] When are .trr files

[gmx-users] When are .trr files essential? (was: Regarding Gromacs output files)

Erik Marklund wrote > On 11 okt 2012, at 16.17, R.Vidya Rajendran (10PHD013) wrote: > >> Hello Friends, >> >> I have two very specific queries regarding gromacs output files. >> >> 1) Since we can generate .xtc file during mdrun, Is is possible to >> stop generating .trr files, because it used t