Re: [gmx-users] Orientation restraints

Bob Johnson wrote: Hello everyone, My system consists of DNA and a carbon nanotube. I would like to restrain the DNA bases in a way that the plane formed by each base is parallel to the z-axis. In other words, I would like to orient the bases such that the normal of each plane is perpendicular to

Re: [gmx-users] MD run error

Kushal Seth wrote: Hi all ! I am running a MD simulation and i got You appear to be trying to do an energy minimization, which although often able to be done by the same code as molecular dynamics, is inherently non-dynamical. Hence it's unwise to confuse matters by referring to one as "MD".

Re: [gmx-users] MD run error

try looking for errors in your pdb file, try double precision EM. it seems that something wrong is with your pdb, because the value of your maximum force. Also check your topology. Good luck Cesar Kushal Seth escribió: Hi all ! I am running a MD simulation and i got "Warning: 1-4 interaction

[gmx-users] configure: error: conditional "am__fastdepCXX" was never defined.

Hi everybody, I've been trying to compile gromacs-3.1.4 onto a linux server with Red Hat v 7.3 OS. I was able to compile the fftw library without incident, but when I issue the configure command (>./configure --prefix=/home/voklejas/gromacs) in the gromacs-3.1.4 directory I get the following

[gmx-users] MD run error

Hi all ! I am running a MD simulation and i got "Warning: 1-4 interaction between 1 and 6 at distance 1.102 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in

Re: [gmx-users] Orientation restraints

Hi Bob, Just a comment: if you don't have a homogeneous DNA sequence (and perhaps even in such a case) you will probably end distorting the sugar-phosphate backbone of the DNA if forcing every base pair to be normal to a common z-axis. Anyway, look for one of these two programs: freehelix (by Di

[gmx-users] Orientation restraints

Hello everyone, My system consists of DNA and a carbon nanotube. I would like to restrain the DNA bases in a way that the plane formed by each base is parallel to the z-axis. In other words, I would like to orient the bases such that the normal of each plane is perpendicular to the z-axis. I don't

[gmx-users] Minimize energy of holoprotein

Hello to everybody, I am new of bioinformatics (I am a computer scientist), but I'm trying to learn. Actually I am working on a model of a holoprotein (protein with "other" molecules), cp26, a transmembrane protein found in tylacoids), modelled for homology (56% identity) from an axisting one (1rw

Re: [gmx-users] inter molecular distance restraints?

Syma, The answer is yes. However, they have to be part of the same molecule "description". That is, they have to be listed in the same [ atoms ] section and so on. You neeed GROMACS to consider them to be part of the same "molecule", which it can do without having bonds between them. David On 4/

Re: [gmx-users] replica exchange doubt

Hi all, I've another question, in the manual (page 39) a REMD calculator is mentioned. Where is it? I've tried to search it on the website without success. Thanks again Andrea ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.

Re: [gmx-users] Re: NS in PME

Janne, You may want to look on the GROMACS developers list for a lot of recent discussion relating to energy conservation. It is a fairly complicated issue. http://www.gromacs.org/pipermail/gmx-developers/ David On 4/11/06, Janne Hirvi <[EMAIL PROTECTED]> wrote: > Thanks for your response David

Re: [gmx-users] replica exchange doubt

Andrea Carotti wrote: Hi all, I've another question, in the manual (page 39) a REMD calculator is mentioned. Where is it? I've tried to search it on the website without success. It's on the TODO list. Thanks again Andrea ___ gmx-users mailing lis

[gmx-users] Re: problems with x2top

From: David van der Spoel <[EMAIL PROTECTED]> Subject: [gmx-users] Re: Problems with x2top To: Steven Kirk <[EMAIL PROTECTED]>, Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Steven Kirk wrote: Hello David, I am havi

RE: [gmx-users] inter molecular distance restraints?

> Thank you for your 30 seconds. > I guess what I was getting as, is there anything I should be aware of when > applying distance restraints (known problems etc) that would have saved me > making common mistakes. Don't know, never done it. > The gromacs manual is good, I would hesitate before say

[gmx-users] modifying replica exchange

Dear gmx developer, I want to modify repl_ex.c for my system. I have read the source code. There is one point I am not clear. In the function replica_exchange( ...), all dynamical information of a system will be exchanged between two replicas when exchanging two replicas is implemented. It looks l

[gmx-users] g_potential problem

Dear Gmxers:   In my simulation, I applied a uniform electric field across the whole system, and I used g_potential -f full -s full -o -sl 200 to observe the voltage drop along z direction.   I am confused with the voltage distribution. What time is it referred to? Or, it is an average over

RE: [gmx-users] inter molecular distance restraints?

Thank you for your 30 seconds. I guess what I was getting as, is there anything I should be aware of when applying distance restraints (known problems etc) that would have saved me making common mistakes. The gromacs manual is good, I would hesitate before saying wonderful Thanks anyway, -Sy

Re: [gmx-users] inter molecular distance restraints?

Besides that, searching through the gromacs user list with keywords like "distance" "restraints" "between" "molecules" would have given some good hits.Tsjerk On 4/11/06, Mark Abraham <[EMAIL PROTECTED]> wrote: > Hi,>> I was just wondering if is possible, in gromacs to apply distance> restraints> be

Re: [gmx-users] inter molecular distance restraints?

> Hi, > > I was just wondering if is possible, in gromacs to apply distance > restraints > between molecules. So I have two ligands (part of the same complex) that I > would like to keep together, even though they are not actually bonded > together. gromacs has a wonderful manual, in which there i

Re: [gmx-users] Re: NS in PME

Janne Hirvi wrote: Thanks for your response David! I tried to simulate bulk water (1372 SPC/E molecules) with your parameters and observed same kind of problems with energy conservation as with my earlier parameters (rlist=rvdw=rcoulomb=1.2 & nstlist=10). In single precision NVE simulation (500p

Re: [gmx-users] replica exchange doubt

Thanks to all for the quick clarifications. Andrea - Original Message - From: "Xavier Periole" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS users" Sent: Tuesday, April 11, 2006 1:55 PM Subject: Re: [gmx-users] replica exchange doubt Andrea Carotti wrote: Hi all gmx-ers, I

Re: [gmx-users] replica exchange doubt

Andrea Carotti wrote: Hi all gmx-ers, I have a doubt concerning the REMD setup. Let's say I want to use 12 cpus to make a REMD at 2 different temp 300 and 400K of the same system. Should I prepare every tpr file with the -np option set to 6? and then run the mdrun with -np 12 -multi -s 300.tpr

RE: [gmx-users] replica exchange doubt

From: "Andrea Carotti" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Subject: [gmx-users] replica exchange doubt Date: Tue, 11 Apr 2006 13:14:51 +0200 Hi all gmx-ers, I have a doubt concerning the REMD setup. Let's say I want to use 12 cpus to make a REMD at 2 differe

[gmx-users] inter molecular distance restraints?

Hi, I was just wondering if is possible, in gromacs to apply distance restraints between molecules. So I have two ligands (part of the same complex) that I would like to keep together, even though they are not actually bonded together. Thanks in advance, -Syma *

[gmx-users] replica exchange doubt

Hi all gmx-ers, I have a doubt concerning the REMD setup. Let's say I want to use 12 cpus to make a REMD at 2 different temp 300 and 400K of the same system. Should I prepare every tpr file with the -np option set to 6? and then run the mdrun with -np 12 -multi -s 300.tpr 400.tpr -replica X -re

[gmx-users] g_dielectric error

Hi, I've some problems in using the command g_dielectric in various example of water(spc ,tip5, tip4).The error appears to be the same for each model;this is for spc water model: Read data set containing 2 colums and 101 rows Assuming (from data) that timestep is 0.1, nxtail = 101 Creating stan

[gmx-users] Re: NS in PME

Thanks for your response David! I tried to simulate bulk water (1372 SPC/E molecules) with your parameters and observed same kind of problems with energy conservation as with my earlier parameters (rlist=rvdw=rcoulomb=1.2 & nstlist=10). In single precision NVE simulation (500ps) drift in total ene

[gmx-users] Local electric field after enerygrp_exl

Dear users:   If I excluded the interactions between two groups through defining "energygrp_excl=Group1 Group2" in mdp file, I am sure no interactions between them during simulation. However, how about the local electric field between these two groups? Is it still existing?   Thanks     Xie