Re: [gmx-users] Steered Molecular Dynamics (SMD) in Gromcas-4.0.5

Hi, you should set one pull group, not 700. The number of atoms in your pull group is 700. Freezing the pull group in x and y direction probably does what you want. Please also consider to upgrade to 4.0.7, which is the most recent stable version. Best, Carsten On Jan 22, 2010, at 7:41 AM, to

RE: [gmx-users] electrostatic forces

Hi, I guess this is caused by the 1-4 interactions. These also contain electrostatic interactions, which are turned off when you turn off the charges, but not by the energygrp_excl option. Berk From: gianfranco.bocchinf...@uniroma2.it To: gmx-users@gromacs.org Date: Thu, 21 Jan 2010 18:58:14 +0

Re: [gmx-users] Lipid parameters for GROMOS96 force fields

Here is another paper related to the secondary structure propensity of different force field. Are current Molecular Dynamics FFs too helical? Best et al: BiophysJ-2008 doi:10.1529/biophysj.108.132696 Note that these papers do not report the unstability of helices in proteins! On Jan 22,

R: [gmx-users] electrostatic forces

Thank you for your reply, Really, I don’t think that the difference come from the 1-4 interactions. I have excluded all the 1-4 interaction involving atoms in the indole group (deleting them from the pairs list). Furthermore, I have added the indole as an energygrps, and checking the 1-4 ener

[gmx-users] Load imbalance

Hi everyone, Lately I've been using gromacs version 3.3.3. Yesterday, I started simulations in a cluster where gromacs version is 4.0.3. After a run, I got this error message: Average load imbalance: 0.5 % Part of the total run time spent waiting due to load imbalance: 0.3 % Steps where the loa

Re: [gmx-users] Load imbalance

Carla Jamous skrev: Hi everyone, Lately I've been using gromacs version 3.3.3. Yesterday, I started simulations in a cluster where gromacs version is 4.0.3. After a run, I got this error message: Average load imbalance: 0.5 % Part of the total run time spent waiting due to load imbalance: 0.

Re: [gmx-users] Load imbalance

Carla Jamous wrote: Hi everyone, Lately I've been using gromacs version 3.3.3. Yesterday, I started simulations in a cluster where gromacs version is 4.0.3. Why start with 4.0.3? You should be using the latest stable version (4.0.7). After a run, I got this error message: Average load i

Re: [gmx-users] Load imbalance

Yes, but I forgot to say that I got this note that followed: 5.4 % performance was lost because the PME nodes had less work to do than the PP nodes. You might want to decrease the number of PME nodes or decrease the cut-off and the grid spacing. Carla On Fri, Jan 22, 2010 at 1:3

Re: [gmx-users] Load imbalance

Carla Jamous wrote: Yes, but I forgot to say that I got this note that followed: 5.4 % performance was lost because the PME nodes had less work to do than the PP nodes. You might want to decrease the number of PME nodes or decrease the cut-off and the grid spacing. 5% loss

Re: [gmx-users] Load imbalance

Well, there you go. That message tells you how to improve performance. Changing the number of PME-nodes to improve performance may or may not be doable, depending on the number of processors availvable. On the other hand, 5.4 % performance loss is not that bad in my oppinion. There is a tool f

[gmx-users] [ dummies 2] or [ virtual_sites 2] not works.

Hi. I'm on QM/MM simulation (gromacs-gaussian03). I exactly followed under reference, but I could't success. http://wwwuser.gwdg.de/~ggroenh/EMBO2004/html/qmmmvacuum.html#top I checked presence of two LA atoms in [ atoms] of TOP file. Also, I checked under [ dummies 2] and [ constraints ]in

[gmx-users] cut-off

Hello, I wanted to know, if say my box is 30A (cubic) and if I set my cut-off lengths i.e. rvdw-switch = 0.8 and rvdw =0.9 , does that mean, the simulation will cut-0ff at 9A? Should I be changing that to 1.5nm (to get half the box cut-off)? I am a little confused about that. Thanks.

Re: [gmx-users] cut-off

nishap.pa...@utoronto.ca wrote: Hello, I wanted to know, if say my box is 30A (cubic) and if I set my cut-off lengths i.e. rvdw-switch = 0.8 and rvdw =0.9 , does that mean, the simulation will cut-0ff at 9A? Should I be changing that to 1.5nm (to get half the box cut-off)? I am a little

Re: [gmx-users] cut-off

I see what you mean, so say if I am doing RDF, the values beyond 9A would be bogus? Quoting "Justin A. Lemkul" : nishap.pa...@utoronto.ca wrote: Hello, I wanted to know, if say my box is 30A (cubic) and if I set my cut-off lengths i.e. rvdw-switch = 0.8 and rvdw =0.9 , does that

Re: [gmx-users] cut-off

nishap.pa...@utoronto.ca wrote: I see what you mean, so say if I am doing RDF, the values beyond 9A would be bogus? To a large extent, probably, but I don't think that I can say that absolutely without context. For example, you've only shown us rvdw, what about rcoulomb? If it is longer

[gmx-users] question

Hi,I want to simulate a finite nono-tubes.Does nonotube be flexible or rigid?which is better?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! Please don't post (u

Re: [gmx-users] question

On 1/22/10 9:11 PM, akram gorji wrote: Hi,I want to simulate a finite nono-tubes.Does nonotube be flexible or rigid?which is better?thanks Do you mean nano tubes? Try some literature search. Quite a bit has been done on this topic, also with GROMACS. -- David. __

[gmx-users] diketopiperazine

Hi, I'm trying to construct diketopiperazine with gromacs. The problem that I have right now is forming the bond that unites the C and N termi to make the cyclic peptide. I tried using specbond.dat but so far I've been unsucessful. Here is my specbond.dat file and pdb file: specbond.dat 8 CYS

Re: [gmx-users] diketopiperazine

Jose Tusell wrote: Hi, I'm trying to construct diketopiperazine with gromacs. The problem that I have right now is forming the bond that unites the C and N termi to make the cyclic peptide. I tried using specbond.dat but so far I've been unsucessful. Here is my specbond.dat file and pdb

Subject: [gmx-users] [ dummies 2] or [ virtual_sites 2] not works.

-0.408 1.528 -1.262 > ATOM 8 CG TRP10.205 -0.166 -2.397 > ATOM 9 CD1 TRP10.227 -1.464 -2.727 > ATOM 10 HD1 TRP1 -0.407 -2.173 -2.195 > ATOM 11 CD2 TRP11.119 0.455 -3.258 > ATOM 12 NE1 TRP1

Re: [gmx-users] diketopiperazine

Thanks Justin, I used specbond.dat with a 0.15nm searching distance to create the bond, it seemed to work. Ramon On Fri, Jan 22, 2010 at 2:40 PM, Justin A. Lemkul wrote: > > > Jose Tusell wrote: > >> Hi, >> >> I'm trying to construct diketopiperazine with gromacs. The problem that I >> have ri

[gmx-users] OPLS force field

Dear Users: I build up my polymer molecules in PRODRG and got the .gro and .itp file. Then anyone knows how I can transfer or edit the itp file into OPLS force field format? Or anyone knows how can I get the OPLS force field parameters if I have my molecule gro file. Any suggestion will be great

Re: [gmx-users] OPLS force field

Yanmei Song wrote: Dear Users: I build up my polymer molecules in PRODRG and got the .gro and .itp file. Then anyone knows how I can transfer or edit the itp file into OPLS force field format? Or anyone knows how can I get the OPLS force field parameters if I have my molecule gro file. An

[gmx-users] Re: Steered Molecular Dynamics (SMD) in Gromcas-4.0.5(toby10222...@sina.com)

Hi Carsten: Thank you for your answers. I don't know whether I am right to reply to gmx-us...@gromacs.org. If I am wrong, please tell me. As in my last letter, I said I was not able to set "pull_weights1" correctly. I have red the mannual, but I don't understand what it tells. I'll do with your

[gmx-users] About "Apply Multiple bonded interactions" for dihedral potential definition

Hi, all, According to Manual v3.3, "It's possible to apply multiple bonded interactions of the same type on the same atoms" [12th line of Page 98]. If a dihedral potential for 4 neighboring atoms is defined 3 times using the "periodic type" in the topology file, like V=k1*(1+cos(phi-phi_s1)) V=k2*

Re: [gmx-users] Re: Steered Molecular Dynamics (SMD) in Gromcas-4.0.5(toby10222...@sina.com)

toby10222...@sina.com wrote: Hi Carsten: Thank you for your answers. I don't know whether I am right to reply to gmx-users@gromacs.org . If I am wrong, please tell me. Yes, keep all discussions on the list for archival purposes (plus, other users can weigh