Re: [gmx-users] Simulation crashes (Gromacs 4.0.5)

Baudilio Tejerina wrote: Hello: I'm trying to run a simulation that crashes with the message below. At this point, I'm not a the level of being able to interpret the error so, I'm uncertain whether is caused by an ill-conditioned model ( input ) or an actual bug in the code. There's a third

Re: [gmx-users] The Cut-off for coulombtype heat up the water system?

Florian Dommert wrote: * Mark Abraham [2009-06-20 11:54:46 +1000]: When I understood the idea of the reaction field correctly, I treat the electrostatic forces with a cutoff and relative dielectric permittivity != 1. With the mentionend Ewald methods I should be able to reproduce exactly the

[gmx-users] Simulation crashes (Gromacs 4.0.5)

Hello: I'm trying to run a simulation that crashes with the message below. At this point, I'm not a the level of being able to interpret the error so, I'm uncertain whether is caused by an ill-conditioned model ( input ) or an actual bug in the code. I would enormously appreciate if someone

Re: [gmx-users] The Cut-off for coulombtype heat up the water system?

* Mark Abraham [2009-06-20 11:54:46 +1000]: When I understood the idea of the reaction field correctly, I treat the electrostatic forces with a cutoff and relative dielectric permittivity != 1. With the mentionend Ewald methods I should be able to reproduce exactly the same circumstances like

Re: [gmx-users] The Cut-off for coulombtype heat up the water system?

Florian Dommert wrote: * Mark Abraham [2009-06-19 14:55:02 +1000]: Chih-Ying Lin wrote: Hi People conclude that the heating up is normal by using a plain cut-off. So, how to fix the problem? 0. Do more background reading. :-) 1. From Berk => use multiple groups. => how ??? => I h

Re: [gmx-users] The Cut-off for coulombtype heat up the water system?

* XAvier Periole [2009-06-20 00:45:55 +0200]: It is simply that if the system is not neutral the Ewald equation are not valid anymore. I would guess that the original papers describe it. I never looked into it. Thanks very much. This should really be the point, because a lattice built just

Re: [gmx-users] What is the important thing when we are watching the MD trajectory movie?

Chih-Ying Lin wrote: Hi What is the important thing when we are watching the MD trajectory movie? Popcorn :-) Seriously, it depends on the objective of the simulation. If you're looking for some rare event to occur and can't define a numerical criterion for which to search, you might watch fo

[gmx-users] What is the important thing when we are watching the MD trajectory movie?

Hi What is the important thing when we are watching the MD trajectory movie? Are people watching the whole trajectory movie? It might take 3-4 hours or longer. What is the efficient way to watch the trajectory movie? Thank you Lin ___ gmx-users mailing

Re: [gmx-users] Having trouble getting gromacs installed.

Dave Hassan wrote: Hello All, I recently downloaded GROMACS and installed it on my Mac using the intructions here: http://www.gromacs.org/WIKI-import/Quick_and_Dirty_Installation. I set my PATH variables, and then tried to follow the getting started section of the website, but I keep gett

[gmx-users] Having trouble getting gromacs installed.

Hello All, I recently downloaded GROMACS and installed it on my Mac using the intructions here: http://www.gromacs.org/WIKI-import/Quick_and_Dirty_Installation. I set my PATH variables, and then tried to follow the getting started section of the website, but I keep getting a 'demo: command not fo

Re: [gmx-users] The Cut-off for coulombtype heat up the water system?

It is simply that if the system is not neutral the Ewald equation are not valid anymore. I would guess that the original papers describe it. I never looked into it. On Jun 19, 2009, at 21:02, Florian Dommert stuttgart.de> wrote: * Mark Abraham [2009-06-19 14:55:02 +1000]: Chih-Ying Lin

Re: [gmx-users] The Cut-off for coulombtype heat up the water system?

Sorry I habe to extend this: Can you please explain me or provide am reference explain why I am not able to use a SPME/PME/PPPM/EwaldSum method for any kind of partial charges living in an environment with periodic boundary conditions ? When I understood the idea of the reaction field correctl

Re: [gmx-users] The Cut-off for coulombtype heat up the water system?

* Mark Abraham [2009-06-19 14:55:02 +1000]: Chih-Ying Lin wrote: Hi People conclude that the heating up is normal by using a plain cut-off. So, how to fix the problem? 0. Do more background reading. :-) 1. From Berk => use multiple groups. => how ??? => I have been thinking that i

Re: [gmx-users] bond constraint

noob noob wrote: Dear all,. I am quite new in MD simulations. I am planning to learn some simple simulation, and now i encounter a little doubt about the bond constraint. I get many references and papers to design a method for my simulation but I cannot get a reference that use "no bond con

[gmx-users] bond constraint

Dear all,. I am quite new in MD simulations. I am planning to learn some simple simulation, and now i encounter a little doubt about the bond constraint. I get many references and papers to design a method for my simulation but I cannot get a reference that use "no bond constraint" in their wor

Re: [gmx-users] g_coord => command not found

Original Message Subject: Re: [gmx-users] g_coord => command not found Date: Fri, 19 Jun 2009 14:41:52 -0400 From: Justin A. Lemkul Reply-To: jalem...@vt.edu Organization: Virginia Tech To: jalem...@vt.edu References: <5777f3840906191128y17c6d3a3jd43b2b637c251...@mail.gmail.co

Re: [gmx-users] g_coord => command not found

Original Message Subject: Re: [gmx-users] g_coord => command not found Date: Fri, 19 Jun 2009 14:41:52 -0400 From: Justin A. Lemkul Reply-To: jalem...@vt.edu Organization: Virginia Tech To: jalem...@vt.edu References: <5777f3840906191128y17c6d3a3jd43b2b637c251...@mail.gmail.co

Re: [gmx-users] g_coord => command not found

Chih-Ying Lin wrote: Hi g_coord is introduced in the Chapter 8 of the Manual. But, when I typed g_coord -h => command not found. What is the NEW name of the g_coord? Which version of the manual? It is not mentioned in version 3.3 or 4.0. If you are looking to extract coordinates, use g

Re: [gmx-users] g_energy => the reasonable range of RMSD or Fluctuation ?

Hi Lin, That depends on the size of your system. Maybe add a book about statistical mechanics and thermodynamics to your reading list... Cheers, Tsjerk On Fri, Jun 19, 2009 at 8:00 PM, Chih-Ying Lin wrote: > HI > Once the system reaches the equilibrium, the thermal properties still > fluctuate

[gmx-users] g_coord => command not found

Hi g_coord is introduced in the Chapter 8 of the Manual. But, when I typed g_coord -h => command not found. What is the NEW name of the g_coord? Thank you Lin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listin

Re: [gmx-users] trjconv -pbc nojump -center rect => does not work

Chih-Ying Lin wrote: Hi I have a protein+several ligand in the simulation box. After 5ns, the protein drift to the right edge of the box and the ligand drift to the left edge of the box. I am very sure that the ligand has attached to the protein. with this command => trjconv -pbc nojum

[gmx-users] g_energy => the reasonable range of RMSD or Fluctuation ?

HI Once the system reaches the equilibrium, the thermal properties still fluctuate within some range. What is the reasonable/trustable range of RMSD or Fluctuation of those thermal properties ? Thank you Lin ___ gmx-users mailing listgmx-users@grom

[gmx-users] trjconv -pbc nojump -center rect => does not work

Hi I have a protein+several ligand in the simulation box. After 5ns, the protein drift to the right edge of the box and the ligand drift to the left edge of the box. I am very sure that the ligand has attached to the protein. with this command => trjconv -pbc nojump -center rect so, ho

Re: [gmx-users] Re: Some questions about OPLS/Berger combination

> The fudge is only applied to generated > pairs. Since we define [ pairtypes ] for all lipid and lipid-water > pairs, fudgeLJ is not applied to those (although fudgeQQ is). Aghhh, this is the piece of information I was missing! Now everything jumps into the right place, thanks :-) ! Somehow the

[gmx-users] Re: Some questions about OPLS/Berger combination

The flaw in your reasoning is a misunderstanding of [ pairtypes ]. Look to section 5.3.4, especially page 99, and 5.7.1, especially page 112, of the gromacs 4 manual. The fudge is only applied to generated pairs. Since we define [ pairtypes ] for all lipid and lipid-water pairs, fudgeLJ is

[gmx-users] gromacs 4.0.4 and 4.0.5

Hi everybody, ___ 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! Please don't post (un)subscribe requests to the list. Use t

[gmx-users] pullx.xvg

Hi, Can anyone please tell me, what the output pullx.xvg actually shows? I used "System" as reference group while pulling in Z- and -Z-direction and the output legend shows 0 Z, 1 dZ, 2 dZ. I would have expected it means the reference group, and the distances to pull group 1 and two, but th

[gmx-users] problem after genion

Dear users, I used genion to neutrilize my system with two Na+ ions. Now with my new .gro and .top file and with a minimization (mdp) input file I try to make a .tpr file with grompp in order to minimize my structure. When I run grompp I get an error > >Program grompp, VERSION 3.3.3 >Source code

[gmx-users] [Fwd: problem after genion]

Sorry. I understood the problem! I included ions.it twice. Thanks, Velia Messaggio Originale Oggetto: problem after genion Data: Fri, 19 Jun 2009 11:21:05 +0200 (CEST) Da: Velia Minicozzi A: gmx-users@gromacs.org Dear users, I used genion to neutrilize my system with two

Re: [gmx-users] g_energy => RMSD = Standard Deviation?

Hi, It also doesn't hurt to read up more about statistics. The standard deviation is the square root of the second central moment of a distribution, so it's the expectation value for the average deviation found in a set of mutually indepent data points. Root mean square deviation does not imply mu

Re: [gmx-users] What can I to do with the problem: lincs warning and water can not be settled?

xiao shijun wrote: hi, The simulation was OK. But when I changed the epsilon of some atoms to get rid of LJ, lincs warning emerged as: step 116 ; time 0.232 LINCS warning ralative constraint deviation after LINCS: rms 0.168

[gmx-users] What can I to do with the problem: lincs warning and water can not be settled?

hi, The simulation was OK. But when I changed the epsilon of some atoms to get rid of LJ, lincs warning emerged as: step 116 ; time 0.232 LINCS warning ralative constraint deviation after LINCS: rms 0.168368, max 4.765960 (betwe

Re: [gmx-users] trjconv -pbc atom -center rect

did you try the option -nojump in trjconv ? On Jun 19, 2009, at 3:56 AM, Chih-Ying Lin wrote: Hi I have a protein+several ligand in the simulation box. After 5ns, the protein drift to the right edge of the box and the ligand drift to the left edge of the box. with this command => trjconv -pbc

Re: [gmx-users] Final Temp = 303 K ?

On Jun 18, 2009, at 11:57 PM, Chih-Ying Lin wrote: Hi Here is my whole md.mdp. But the final Temp = 303 K No matter I extend the simulation time, the final Temp = 303 K and it can not reach the ref_t = 300 K Does it make sense? Yes unfortunately the 303 K is what you should expect. This is sm