[gmx-users] Position restraint of crystal waters

Hi gmxusers, Hope you are well. I am trying to apply position restraints to my crystal waters (just briefly, 1-2ns) but have been unsuccessful. Taking into account the advice from this thread http://lists.gromacs.org/pipermail/gmx-users/2012-February/068780.html, this was what I had done:

RE: [gmx-users] Energy minimization of crystal structure with water

of crystal structure with water On 18/03/2012 1:01 PM, NG HUI WEN wrote: Hi all, I have a seemingly simple task that turned quite tricky here. I am trying to perform energy minimization on a crystal structure after adding hydrogen to the protein using pdb2gmx (OPLS). The problem I am facing now

[gmx-users] Energy minimization of crystal structure with water

Hi all, I have a seemingly simple task that turned quite tricky here. I am trying to perform energy minimization on a crystal structure after adding hydrogen to the protein using pdb2gmx (OPLS). The problem I am facing now is that after energy minimization, the protein and water

RE: [gmx-users] Distance Restraints on Protein - possible at all?

To: Discussion list for GROMACS users Subject: Re: [gmx-users] Distance Restraints on Protein - possible at all? On 22/02/2012 11:17 AM, NG HUI WEN wrote: From: NG HUI WEN Sent: Sunday, February 19, 2012 1:19 PM To: gmx-users@gromacs.orgmailto:gmx-users@gromacs.org Subject: Distance Restraints on Protein

[gmx-users] Distance Restraints on Protein - possible at all?

From: NG HUI WEN Sent: Sunday, February 19, 2012 1:19 PM To: gmx-users@gromacs.org Subject: Distance Restraints on Protein - possible at all? Dear gmxusers, I have been trying to apply distance restraints on my protein but have been unsuccessful thus far. I have consulted the user forum

RE: [gmx-users] questions on distance restraints

-users-boun...@gromacs.org] on behalf of NG HUI WEN [huiwen...@nottingham.edu.my] Sent: 18 January 2012 16:40 To: Discussion list for GROMACS users Subject: RE: [gmx-users] questions on distance restraints Dear Tsjerk, Thanks very much indeed for confirming this, really appreciate it. I will do

RE: [gmx-users] questions on distance restraints

To: Discussion list for GROMACS users Subject: Re: [gmx-users] questions on distance restraints NG HUI WEN wrote: Dear all, Apologies for getting back to this topic again - am still having trouble trying to get distance restraints to work on my protein. Following Tsjerk's advice, I have

RE: [gmx-users] questions on distance restraints

through the information in the .tpr file given by gmxdump to see if they are indeed properly defined. Cheers, Tsjerk On Jan 18, 2012 1:46 AM, NG HUI WEN huiwen...@nottingham.edu.mymailto:huiwen...@nottingham.edu.my wrote: Dear gmxusers, I have some questions about distance restraints that I

[gmx-users] questions on distance restraints

Dear gmxusers, I have some questions about distance restraints that I hope you would be able to shed some light on. Thanks in advance. I am trying to apply distance restraints to my protein. Below was what I did: -use genrestr to create my ca_disre.itp genrestr -f membedded_em.gro -o

[gmx-users] Visualizing g_helixorient output

Dear all, I have a follow up question from this recent post http://www.mail-archive.com/gmx-users@gromacs.org/msg45736.html regarding the visualization of g_helixorient output. According to the post, one needs to use xmgrace with -nxy to view the data properly. I have not got the xmgrace

RE: [gmx-users] Visualizing g_helixorient output

...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Thursday, November 24, 2011 10:39 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Visualizing g_helixorient output On 23/11/2011 8:59 PM, NG HUI WEN wrote: Dear all, I have a follow up question from

[gmx-users] Failure to preserve simulation temperature

Hi all, I have something here which I am would like to pick your brains. Thank you in advance. In my trial-and-error attempt to equilibrate my membrane protein system, I encountered this problem. I was playing with 2 different mdp files (in succession), first by using the Nose Hoover then

[gmx-users] nstcomm set to 10

Dear gmxusers, I have a question here concerning nstcomm. I got the note below after doing grompp, I'd like to do something about it. NOTE 1 [file HW_NPT.mdp]: nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy Currently, my nstcomm is

RE: [gmx-users] using Berger Lipids in gromacs 4.5.3

a lot! HW -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Sunday, January 23, 2011 9:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] using Berger Lipids in gromacs 4.5.3 NG HUI WEN

RE: [gmx-users] using Berger Lipids in gromacs 4.5.3

...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Monday, January 24, 2011 10:14 PM To: Gromacs Users' List Subject: Re: [gmx-users] using Berger Lipids in gromacs 4.5.3 NG HUI WEN wrote: Dear Justin, Thanks for pointing out :) much appreciated. I tried selecting 1 and the process

RE: [gmx-users] using Berger Lipids in gromacs 4.5.3

It worked! Thanks very much again for your time and help. Cheers, huiwen -Original Message- From: Justin A. Lemkul [mailto:jalem...@vt.edu] Sent: Tuesday, January 25, 2011 8:49 AM To: NG HUI WEN; Gromacs Users' List Subject: Re: [gmx-users] using Berger Lipids in gromacs 4.5.3

[gmx-users] using Berger Lipids in gromacs 4.5.3

Dear all, This must be a pretty simple problem but I am stuck nonetheless. I have been using the lipids from Prof Tieleman's website without any problem on gromacs 4.0.7. Now that I've got 4.5.3 installed, I want to try the g_membed tool but have encountered these problems. Following

RE: [gmx-users] using Berger Lipids in gromacs 4.5.3

Oops sorry! I found the mistake... the topology file should read gromos53a6_lipid.ff/forcefield.itp instead of gromos53a6.ff/forcefield.itp silly me From: gmx-users-boun...@gromacs.org on behalf of NG HUI WEN Sent: Sun 1/23/2011 1:40 PM To: gmx-users

RE: [gmx-users] Replicating an experiment

/2010 4:37 AM, NG HUI WEN wrote: Thank you David for your prompt and useful reply :) I am in fact simulating a membrane protein. It's good to know I can use the generate-new-starting-velocity method. But, do you mind to elaborate a bit more what you mean by if you simulate long enough? I would

[gmx-users] Replicating an experiment

Dear all, Merry Xmas! I have a very quick question here which i'd like to pick your brain on, would really appreciate a reply. I am planning to replicate an experiment that I have carried out. Just wondering what is the best way to do it? I am thinking of changing the starting velocity of

RE: [gmx-users] Replicating an experiment

12/25/2010 10:28 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Replicating an experiment On 2010-12-25 15.05, NG HUI WEN wrote: Dear all, Merry Xmas! I have a very quick question here which i'd like to pick your brain on, would really appreciate a reply. I am planning

RE: [gmx-users] Replicating an experiment

Got it, thanks very much David! :) -Original Message- From: gmx-users-boun...@gromacs.org on behalf of David van der Spoel Sent: Sun 12/26/2010 5:55 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Replicating an experiment On 12/25/10 6:37 PM, NG HUI WEN wrote

RE: [gmx-users] Illegal division by zero at inflategro

Try POP instead of POPE :) From: gmx-users-boun...@gromacs.org on behalf of shikha agarwal Sent: Thu 12/23/2010 4:21 PM To: gmx-users@gromacs.org Subject: [gmx-users] Illegal division by zero at inflategro Hi I am having a trouble during inflategro

RE: [gmx-users] mdrun -rerun: bonded interactions of protein

for GROMACS users Subject: Re: [gmx-users] mdrun -rerun: bonded interactions of protein On 11/11/2010 7:46 PM, NG HUI WEN wrote: Thanks a lot Justin and Mark for your useful input. Indeed Justin was right, the quest to dissect the total energy of the system to get that contributed

RE: [gmx-users] mdrun -rerun: bonded interactions of protein

: RE: [gmx-users] mdrun -rerun: bonded interactions of protein Quoting NG HUI WEN huiwen...@nottingham.edu.my: Dear Mark and Justin, I have a potentially silly question here. I have been trying to work out the figures from the various options of g_energy. You mentioned before that the bonded

[gmx-users] Area per lipid calculation

Dear gromacs users, I have a protein embedded in a lipid bilayer. After sufficient equilibration of the system ( i.e. size of box X and Box Y became quite constant), I would now like to assess the area per lipid of my system. However, (I think) I could not simply do this ( average size

RE: [gmx-users] mdrun -rerun: bonded interactions of protein

: bonded interactions of protein On 10/11/2010 11:29 PM, NG HUI WEN wrote: Hi Gmxusers, I have been trying to run mdrun -rerun to get the energy of the protein in my protein-lipid system. I know similar questions have been raised on this topic before, I have tried to glean useful information

[gmx-users] Multiple position restraints on the same system

Dear GMXusers, I am trying to perform NVT on my solvated protein-lipid system. After inserting the protein into the lipid using inflategro and a round of energy minimization, I performed a 100ps NVT with position restraint only on the protein molecule using (posre.itp). After 100ps of NVT,

RE: [gmx-users] Equilibration of POPC - Lipid molecules jump outof box

molecules jump outof box NG HUI WEN wrote: Dear gmxusers, I have obtained a box of POPC with a starting dimension of 12.48, 12.36, and 6.92 (nm) using genconf -nbox 2 2 1. The original lipid was downloaded from Prof. Tieleman's site (popc128a.pdb). My intention

[gmx-users] Equilibration of POPC - Lipid molecules jump out of box

Dear gmxusers, I have obtained a box of POPC with a starting dimension of 12.48, 12.36, and 6.92 (nm) using genconf -nbox 2 2 1. The original lipid was downloaded from Prof. Tieleman's site (popc128a.pdb). My intention is to equilibrate the new bilayer such that the lipids,

RE: [gmx-users] How to make a lipid bilayer with specific dimensions?

* Previous message: [gmx-users] How to make a lipid bilayer with specific dimensions? * Next message: [gmx-users] Query regarding protonation and deprotonation of some residues * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] NG HUI WEN wrote: Dear gmxusers, I am

RE: [gmx-users] How to make a lipid bilayer with specific dimensions?

with specific dimensions? NG HUI WEN wrote: Thanks for that guys! I will try them out. Just a quick question here with regards to my lipids being possibly too small, does it have something to do with the minimum image criterion for PBC? I have ensured that the distance of edge of the box

RE: [gmx-users] Energy Minimzation with Gromacs leads to distortionofplanar groups

leads to distortionofplanar groups NG HUI WEN wrote: Hi Thanks a lot for the suggestions. I removed -DFLEXIBLE this time but it still didn't work unfortunately. I started off with 0 distorted planar group and ended up with 38 after minimization (same as before). Justin, the values were

RE: [gmx-users] Energy Minimzation with Gromacs leads to distortionof planar groups

...@gromacs.org] On Behalf Of NG HUI WEN Sent: 20 September 2010 04:21 To: gmx-users@gromacs.org Subject: [gmx-users] Energy Minimzation with Gromacs leads to distortion of planar groups Dear Gmxusers, I have noticed that energy minimization with gromacs (gromos G53a6 forcefield) had led

[gmx-users] Energy Minimzation with Gromacs leads to distortion of planar groups

Dear Gmxusers, I have noticed that energy minimization with gromacs (gromos G53a6 forcefield) had led to the distortion of sidechain planarity in my protein model. Comparison of PROCEHCK results between the pre- and post energy minimized structures have shown an increase in the number of

[gmx-users] Attempting to scale gromacs mdrun_mpi

Hi, I have been playing with the mdrun_mpi command in gromacs 4.0.7 to try out parallel processing. Unfortunately, the results I got did not show any significant improvement in simulation time. Below is the command I issued: mpirun -np x mdrun_mpi -deffnm where x is the number of

[gmx-users] RE: Large output files and limited disk space. How do I handle them?

Hi guys Thanks for your help! I will consider your suggestions. Huiwen From: NG HUI WEN Sent: Monday, August 09, 2010 11:05 AM To: gmx-users@gromacs.org Subject: Large output files and limited disk space. How do I handle them? Dear gmxusers, I have a very basic question here

[gmx-users] Large output files and limited disk space. How do I handle them?

Dear gmxusers, I have a very basic question here which I hope someone could help me with. I was running a couple of simulations over the weekend on a shared cluster and both came to a stop for the same reasons: Program mdrun_mpi, VERSION 4.0.7 Source code file: trnio.c, line: 252 File

[gmx-users] pdb2gmx renumbers the residues in my pdb file

Hi, I'm a new gromacs user. I have encountered a problem with pdb2gmx where it automatically renumbers the residues in my pdb file. For instance, the first residue in my protein F8 has become F1 - this affects all the residues in the protein, something I find rather inconvenient. I've

RE: [gmx-users] pdb2gmx renumbers the residues in my pdb file

file - Original Message - From: NG HUI WEN huiwen...@nottingham.edu.my Date: Thursday, June 3, 2010 18:08 Subject: [gmx-users] pdb2gmx renumbers the residues in my pdb file To: gmx-users@gromacs.org Hi, I'm a new gromacs user. I have encountered a problem with pdb2gmx where