[gmx-users] salt bridge

I would like to calculate the bindings that occur at the same time during my md trajectory. i.e. The binding between an atom of a residue of the protein and water molecule and the binding between the same water molecule with another atom of a residue of the DNA. I need to also identify which

[gmx-users] salt bridge

Dear gmx-users, I would like to calculate the bindings that occur at the same time during my md trajectory. i.e. The binding between an atom of a residue of the protein and water molecule and the binding between the same water molecule with another atom of a residue of the DNA. I need to also

[gmx-users] Position restraints

Dear gmx-users, I am trying to simulate a thermalized wall in the framework of CG Martini force field. To do this I am planning to link my wall atoms to some reference points (initial positions) by harmonic potentials. From what I have found in the manual it looks like this can be done by

Re: [gmx-users] Position restraints

Mikhail Stukan wrote: Dear gmx-users, I am trying to simulate a thermalized wall in the framework of CG Martini force field. To do this I am planning to link my wall atoms to some reference points (initial positions) by harmonic potentials. From what I have found in the manual it looks

[gmx-users] Different g_sas values between AMBER, CHARMM and GROMOS ff for DPC

Dear All, I have simulated three DPC micelles with the same size (54 lipids) with different force fields (CHARMM, AMBER et GROMOS53A6) and computed the average accessible surface areas for each lipids with g_sas (gmx4.5.3) I obtain the three average values for total DPC, the headgroup

Re: [gmx-users] Different g_sas values between AMBER, CHARMM and GROMOS ff for DPC

On 2011-04-09 19.06, sa wrote: Dear All, I have simulated three DPC micelles with the same size (54 lipids) with different force fields (CHARMM, AMBER et GROMOS53A6) and computed the average accessible surface areas for each lipids with g_sas (gmx4.5.3) I obtain the three average values for

[gmx-users] molecule type

dear Justin, I should appreciate your guides in this period. They're really helpful but again, I have some problem: I started over, several times as you suggested. I replaced the name of SOL with N2. The problem of coordinates was solved by manual addition of #N2 molecules to topol.top each

Re: [gmx-users] molecule type

sarah k wrote: dear Justin, I should appreciate your guides in this period. They're really helpful but again, I have some problem: I started over, several times as you suggested. I replaced the name of SOL with N2. The problem of coordinates was solved by manual addition of #N2

Re: [gmx-users] molecule type

Justin A. Lemkul wrote: sarah k wrote: dear Justin, I should appreciate your guides in this period. They're really helpful but again, I have some problem: I started over, several times as you suggested. I replaced the name of SOL with N2. The problem of coordinates was solved by

Re: [gmx-users] Naming of DNA residues, and structure of .pdb file

majid hasan wrote: Dear All, I am trying to make sure that the names of dna residues in my .pdb file match with .rtp file in the Amber forcefield. I looked up the residuetypes.dat file (attached), and it gives the names for DNA residues, which are of the form, DX, DX3, DX5, DXN

Re: [gmx-users] Naming of DNA residues, and structure of .pdb file

Okay, thanks a lot. Majid From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sat, April 9, 2011 3:05:48 PM Subject: Re: [gmx-users] Naming of DNA residues, and structure of .pdb file majid hasan wrote:

Re: [gmx-users] Error while performing a REMD simulation

On 09/04/11 06:34, Luis Miguel Medina Solano wrote: Hello, Right now I'm trying to perform a REMD simulation of a poly-alanine peptide, using 43 replicas ranging from 300-500 K. the procedure I'm using is the following: 1. Energy minimization of the peptide in vacuum 2. generation of the

Re: [gmx-users] g_cluster: optimal cutoff

On 05/11/10 10:57, Fabio Affinito wrote: On 10/31/2010 08:20 PM, Valeria Losasso wrote: Dear all, for my cluster analysis I am using the g_cluster tool with the gromos method. The problem is that I have to compare the results for system of different lengths, and of course the result of the

Re: [gmx-users] Still model

Hi Yuguang, Thanks for the input. For the AMBER vs GROMACS comparison, what GB model you were using, OBC, HCT, or Still. Also, do you notice any source code questions that I mentioned ? Thanks Regard, Chi-cheng On Fri, Apr 8, 2011 at 10:24 PM, Mu Yuguang (Dr) y...@ntu.edu.sg wrote: Dear

Re: [gmx-users] Still model

On 9/04/2011 1:24 PM, Mu Yuguang (Dr) wrote: Dear Chi-Xheng, We have tried GB module in gromacs, but unfortunately we found something wrong with it. What we found is that the results got from gromacs were quite different from those obtained from AMBER codes. We did not check in details

Re: [gmx-users] aminoacids.n.tdb

On 8/04/2011 11:25 PM, Emine Deniz Tekin wrote: Hi Gromacs users, I want to covalently link the lauroic acid to the Valine residue (it is a peptide (amide) bond), I know that I should update the specbond.dat.But before updating this file, I need the NH as an N terminal of the first residue

Re: [gmx-users] multicomponent system- units

On 8/04/2011 12:18 PM, Elisabeth wrote: Hello everyone, I have encountered a simple problem. For a homogenous system what g_energy reports is dependent on the system size and one needs to use -nmol option to divide energies by number of molecules to obtain per mol values. I am attempting

Re: [gmx-users] Error while performing a REMD simulation

Hi Luis, First of all, NEVER REPLY IN PRIVATE when dealing with a mailing list thread. It's a serious breach of netiquette. Mailing lists are designed to be public and searchable. People help other people on a mailing list so that the answer is public and other people can look for the

Re: [gmx-users] Error while performing a REMD simulation

On 10/04/2011 10:58 AM, devicerandom wrote: Hi Luis, First of all, NEVER REPLY IN PRIVATE when dealing with a mailing list thread. It's a serious breach of netiquette. Mailing lists are designed to be public and searchable. People help other people on a mailing list so that the answer is

Re: [gmx-users] Error while performing a REMD simulation

Hello, I'm very sorry for the way I reply, the truth is that i didn't know how else to reply (it is my first time posting here). the script to generate the REMD is: #!/bin/bash # ff opsla and water spc # echo -e 14\n4\n3\n3 0 |pdb2gmx -f 1.pdb -o inib4em.pdb -p topol.top -ignh -ter

Re: [gmx-users] Error while performing a REMD simulation

Luis Miguel Medina Solano wrote: Hello, I'm very sorry for the way I reply, the truth is that i didn't know how else to reply (it is my first time posting here). the script to generate the REMD is: #!/bin/bash # ff opsla and water spc # echo -e 14\n4\n3\n3 0 |pdb2gmx -f 1.pdb -o

Re: [gmx-users] Error while performing a REMD simulation

Hello, I used a -maxwarn 5, but I only obtain 1 warning, (about obsolete entries that the .mdp file has). I used a solute-box distance of 0.34 in order to reduce the simulation box. I used before a solute-box distance of 1 nm and the problem persist. my .mdp file is the next: ; VARIOUS

Re: [gmx-users] Error while performing a REMD simulation

Luis Miguel Medina Solano wrote: Hello, I used a -maxwarn 5, but I only obtain 1 warning, (about obsolete entries that the .mdp file has). I used a solute-box distance of 0.34 in order to reduce the simulation box. I used before a solute-box distance of 1 nm and the problem persist.

Re: [gmx-users] Error while performing a REMD simulation

On 10/04/2011 11:44 AM, Justin A. Lemkul wrote: Maybe this is unrelated to the underlying problem, but hopefully it helps in the long run. Nothing worse than a reviewer saying, Nice project, but 100% of the data are junk. Bad idea, and 100% of the data are junk ? :-) Mark -- gmx-users

[gmx-users] Dangling bond error for dna

Dear All, I created .pdb file for dna using gabedit. But when I try to create the topology file I get this error: Fatal error: There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb file.

Re: [gmx-users] Dangling bond error for dna

majid hasan wrote: Dear All, I created .pdb file for dna using gabedit. But when I try to create the topology file I get this error: Fatal error: There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb

Re: [gmx-users] Dangling bond error for dna

.pdb file size was big, so message didn't deliver. Now I have removed atoms from pdb file to reduce the size, and the files are attached. Thanks, Majid From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: