[gmx-users] Converting Gromacs output files to dl_poly output files.

2010-02-23 Thread naimah haron naimah
Dear Gromacs users, I simulated ionic liquids by GROMACS code. The force field that I used was OPLS-AA. Now, I like continuous my work on these ionic systems by DL_POLY code. Have anyone know the proper/simple way for converting GROMACS output files to DL_POLY output. Thanks IMA --

[gmx-users] Query about g_hbond

2010-02-23 Thread naimah haron naimah
Dear gmx-users... I am new to gromacs, I am trying to obtain the intermolecular hydrogen bonds formed during 10ns simulation of 125 ionic liquid (tetraethylammonium L-Lysinate). I use OPLS-AA force field for this simulation. When I do this by using g_hbond and selecting the LYS group, I am gett

Re: [gmx-users] water simulation

2010-02-23 Thread Justin A. Lemkul
Amit Choubey wrote: Hi everyone, I am afraid this is not really a gromacs related question. Could anyone refer me to a review paper which discusses about simulating water? Does any of them gives a comparative and complete study of molecular dynamics with water , answering questions like whi

[gmx-users] water simulation

2010-02-23 Thread Amit Choubey
Hi everyone, I am afraid this is not really a gromacs related question. Could anyone refer me to a review paper which discusses about simulating water? Does any of them gives a comparative and complete study of molecular dynamics with water , answering questions like which water model to use, how

Re: [gmx-users] (no subject)

2010-02-23 Thread Mark Abraham
On 24/02/2010 12:23 AM, Antonia V. wrote: Dear all, I am simulating a two component system and I want to calculate the g(r) of the centers of mass of the one component. Using the command, g_rdf -f traj.xtc -rdf mol_com I get an rdf which doesn't obtain the value one at long distances. How can

Re: [gmx-users] ffamber94 with gromacs 4.0.3

2010-02-23 Thread Mark Abraham
On 24/02/2010 12:56 AM, Justin A. Lemkul wrote: Carla Jamous wrote: Hi, please does anyone know if the ffamber94 force-field is compatible with gromacs version 4.0? Because I used to use it with gromacs 3.3.3 but now that I'm trying with gromacs 4, I'm having some error messages. There is n

Re: [gmx-users] Re: Inconsisten shift Error

2010-02-23 Thread Justin A. Lemkul
tekle...@ualberta.ca wrote: Hi Justin, My system is -- simulation a polymer (called PAP) in toluene (TOL)... to see the aggregation behavior of the molecule in TOL. the PAP molecule contains 55 atoms... I inserted 8 PAP molecule in a Toluene . it works fine. Energy minimization .

[gmx-users] Reducing distance between atoms! PULL

2010-02-23 Thread Алексей Раевский
Sorry, I want to ask the same question I had a week ago. I need your advice in COM PULL. This is a part of article which describes methodology "...with respect to the atomic distance between the carbonyl carbon of the substrate and the oxygen atom of the identified nucleophilic water, a constraine

Re: [gmx-users] hydrogen bond autocorrelation function c(t),

2010-02-23 Thread Erik Marklund
leila karami skrev: Hi In hydrogen bond autocorrelation function c(t), correlation of what quantity of hydrogen bond is considered? thanks Its existence. Erik -- --- Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell a

[gmx-users] Re: Inconsisten shift Error

2010-02-23 Thread Justin A. Lemkul
tekle...@ualberta.ca wrote: Hi Justin, I just checked this error on the archive list but could not found a reasonable answer .. I have done the energy minimization and it is ok Fmax less than 100 but when I start equilibrating my system I got the following error.. ===

[gmx-users] Inconsisten shift Error

2010-02-23 Thread teklebrh
Hi Justin, I just checked this error on the archive list but could not found a reasonable answer .. I have done the energy minimization and it is ok Fmax less than 100 but when I start equilibrating my system I got the following error.. =

Re: [gmx-users] problem in npt pr for pope

2010-02-23 Thread Justin A. Lemkul
Mahnam wrote: In God We Trust Hello everyone We have a problem for equilibrate the system with a protein within POPE. we have searched mailing list , we dident any good note. We have used pope.pdb from Dr. Tielemans website. We have inserted our protein into pope and minimized it and equilibr

Re: [gmx-users] ffamber94 with gromacs 4.0.3

2010-02-23 Thread deisy yurley rodriguez sarmiento
Yes, the force field Amber94 is compatible with Gromacs 4.0, i use that combination...you should are very careful whit the instalation. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.groma

Re: [gmx-users] problem in g_rdf using only x and y

2010-02-23 Thread Justin A. Lemkul
Rebeca García Fandiño wrote: Hi, thank you very much for your answer. However, I have tried with the 4.0.7 version, and the problem continues, and it is just the same. I have the trajectory and tpr file obtained with the 4.0.4 version. Do you think it cares, or maybe is it another problem?

RE: [gmx-users] problem in g_rdf using only x and y

2010-02-23 Thread Rebeca García Fandiño
Hi, thank you very much for your answer. However, I have tried with the 4.0.7 version, and the problem continues, and it is just the same. I have the trajectory and tpr file obtained with the 4.0.4 version. Do you think it cares, or maybe is it another problem? Cheers, Rebeca. From: g...@hotma

RE: [gmx-users] problem in g_rdf using only x and y

2010-02-23 Thread Berk Hess
Hi, I fixed this bug in 4.0.7. Berk From: rega...@hotmail.com To: gmx-users@gromacs.org Date: Tue, 23 Feb 2010 15:40:07 + Subject: [gmx-users] problem in g_rdf using only x and y Hi, I am trying to calculate g_rdf using only the x and y components of the distance (gromacs 4.0.4):

[gmx-users] problem in g_rdf using only x and y

2010-02-23 Thread Rebeca García Fandiño
Hi, I am trying to calculate g_rdf using only the x and y components of the distance (gromacs 4.0.4): g_rdf -f trajectory.xtc -s production1.tpr -n index.ndx -o rdf_Na_xy.xvg -com -norm -pbc -xy and the calculations stays at the window: Select a group: 1 Selected 1: 'UNK' Select a group: 4 Sel

[gmx-users] problem in npt pr for pope

2010-02-23 Thread Mahnam
In God We Trust Hello everyone We have a problem for equilibrate the system with a protein within POPE. we have searched mailing list , we dident any good note. We have used pope.pdb from Dr. Tielemans website. We have inserted our protein into pope and minimized it and equilibrated it with NVT

[gmx-users] rdf not equal to one

2010-02-23 Thread Antonia V .
Dear all, I am simulating a two component system (which form two completely separated phases) and I want to calculate the g(r) of the centers of mass of the one component. Using the command, g_rdf -f traj.xtc -rdf mol_com I get an rdf which doesn't obtain the value one at long distances.

Re: [gmx-users] hydrogen bond autocorrelation function c(t),

2010-02-23 Thread Justin A. Lemkul
leila karami wrote: Hi In hydrogen bond autocorrelation function c(t), correlation of what quantity of hydrogen bond is considered? thanks There is a reason Gromacs tools frequently print out a message saying "please read and cite the following reference." I would suggest you start

[gmx-users] hydrogen bond autocorrelation function c(t),

2010-02-23 Thread leila karami
Hi In hydrogen bond autocorrelation function c(t), correlation of what quantity of hydrogen bond is considered? thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting

Re: [gmx-users] ffamber94 with gromacs 4.0.3

2010-02-23 Thread Justin A. Lemkul
Carla Jamous wrote: Hi, please does anyone know if the ffamber94 force-field is compatible with gromacs version 4.0? Because I used to use it with gromacs 3.3.3 but now that I'm trying with gromacs 4, I'm having some error messages. There is no problem at all using ffamber under Gromacs 4

[gmx-users] ffamber94 with gromacs 4.0.3

2010-02-23 Thread Carla Jamous
Hi, please does anyone know if the ffamber94 force-field is compatible with gromacs version 4.0? Because I used to use it with gromacs 3.3.3 but now that I'm trying with gromacs 4, I'm having some error messages. Thank you Carla -- gmx-users mailing listgmx-users@gromacs.org http://lists.grom

[gmx-users] (no subject)

2010-02-23 Thread Antonia V .
Dear all, I am simulating a two component system and I want to calculate the g(r) of the centers of mass of the one component. Using the command, g_rdf -f traj.xtc -rdf mol_com I get an rdf which doesn't obtain the value one at long distances. How can I change that? thank you for your help,

Re: [gmx-users] protein in dppc

2010-02-23 Thread Justin A. Lemkul
edmund lee wrote: Dear Justin and all.. I have been struggled for the pass few weeks... I follow the KALP-15 in DPPC tutorials but I am using my own protein instead. I had successfully reached the step INFLATEGRO where 2 lipid removed from the upper layer n 2 lipids removed from the lower

Re: [gmx-users] temperature

2010-02-23 Thread Itamar Kass
Hi Shahab, The best temperature to use is 298K as this is the temperature in which the force filed was parameterised. But, and this is a big but, I speculate that any errors you might have during the simulation due to the use of 310K is minimal and less then other inaccuracies in the force field.

[gmx-users] temperature

2010-02-23 Thread shahab shariati
Hi gromacs users I want to run simulation of protein-dna interaction. what is best for temperature in mdp file: 1) 300K (default) 2) 310k (physiologic temperature) Any help will highly appreciated! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx

Re: [gmx-users] Are you know the way for converting dl_poly input files to Gromacs inputs

2010-02-23 Thread Florian Dommert
Hello, at first I want to warn you the Lopes Force field for Ionic Liquids has some real defficiencies, especially in terms of reproducing correct dynamics. Now it depends on the counterion you want to use. For Ntf2 the is a force field from the Group of Ralf Ludwig, that give correct dynamics

[gmx-users] Re: 2. protein in dppc (edmund lee)

2010-02-23 Thread Gerrit Groenhof
Hi, If I am allowed to do some advertisement: you could try the tool g_membed for inserting proteins as well http://wwwuser.gwdg.de/~ggroenh/membed.html Gerrit gmx-users-requ...@gromacs.org wrote: >2. protein in dppc (edmund lee) > > Date: Tue, 23 Feb 2010 15:55:36 +0800 > From: edmund le

Re: [gmx-users] writing forces in gromacs

2010-02-23 Thread Amit Choubey
Hi Berk. Thanks a lot. I did not know that. Amit On Mon, Feb 22, 2010 at 11:57 PM, Berk Hess wrote: > Hi, > > This note is printed when output files will be "large", large is defined as > more than 2 GB. > Not writing forces just gets you under this limit. > > Berk > > ---

Re: [gmx-users] Cut-offs in gromacs

2010-02-23 Thread David van der Spoel
Lum Nforbi wrote: Dear all, I did two md simulations of 200 particles each of a lennard-jones fluid. One of them gave me the correct pair distribution function for a lennard-jones fluid (converging to 1) and one did not (converging to zero). I have attached the .mdp files for both sy