Re: [gmx-users] Fwd: -pbc nojump

Right :) On Wed, Oct 27, 2010 at 2:27 PM, leila karami wrote: > Dear Tsjerk > > Thus, as you said, Xtc file obtained from trjconv –pbc nojump only concerns > visualization. Thus, can I use old xtc file (with out –pbc nojump) for > analysis such as interfacial waters and water mediated hydrogen bo

[gmx-users] Fwd: -pbc nojump

Dear Tsjerk Thus, as you said, Xtc file obtained from trjconv –pbc nojump only concerns visualization. Thus, can I use old xtc file (with out –pbc nojump) for analysis such as interfacial waters and water mediated hydrogen bonds or every other analysis? -- gmx-users mailing listgmx-users@gro

Re: [gmx-users] Fwd: -pbc nojump

Hi Leila, 2.xtc should contain all that you want. My point was that you shouldn't need to separate protein/dna and solvent into two trajectories to be combined later. Note that this only concerns visualization. You can do distance and H-bond calculations on the original trajectory, as the relevant

[gmx-users] Fwd: -pbc nojump

Dear Carsten and David and Tsjerk Thanks for your time and attention My purpose of these questions is to find a way that 1) close two separated strand of dna (in my case only –pbc nojump fix it) and also 2) water molecules to be put in interface of between protein and dna. Because I want to sur

[gmx-users] Fwd: -pbc nojump

Dear Tsjerk I did what you said: 1. trjconv -f a.xtc -s a.tpr -o 1.xtc -pbc nojump (system for output) 2. trjconv -f a.xtc -s a.tpr -o 2.xtc -pbc mol –center (pr/dna for centering, system for output) Now, I need new trajectory file for analysis. How I obtain new trajectory file fr

Re: [gmx-users] Fwd: -pbc nojump

Hi Leila, Maybe you're better off trying: 1. trjconv -pbc nojump # choose system for output 2. trjconv -center -pbc mol # choose protein/dna for centering, system for output Centering is done before removing PBC, so you should be safe with two passes. You might also want to play with -ur t

Re: [gmx-users] Fwd: -pbc nojump

On Oct 27, 2010, at 10:05 AM, leila karami wrote: > Hi Carsten > > Thanks for your answer. You got my case very well. > > I understand your mean as follows: > > 1) Trjconv –f a.xtc –s a.tpr –o b.xtc –pbc mol (output group=water) > > 2) Trjconv –f a.xtc –s a.tpr –o c.xtc –pbc noju

[gmx-users] Fwd: -pbc nojump

Hi Carsten Thanks for your answer. You got my case very well. I understand your mean as follows: 1) Trjconv –f a.xtc –s a.tpr –o b.xtc –pbc mol (output group=water) 2) Trjconv –f a.xtc –s a.tpr –o c.xtc –pbc nojump (output group =protein-dna) Is that true? You said, (Then over

Re: [gmx-users] Fwd: -pbc nojump

Hi, with the nojump option, your water molecules will slowly diffuse out of the "home" box and appear far away from your protein if you display the MD system with VMD or pymol. You can split your trajectory in two parts (using index groups) and use different options on them individually: a) on th

Re: [gmx-users] Fwd: -pbc nojump

On 2010-10-27 09.40, David van der Spoel wrote: I did simulation of protein-dna complex in water solvent. After simulation, two strands of dna was separated when I displayed my a.xtc with VMD.I used (trjconv –f a.xtc –s a.tpr –n a.ndx –o b.xtc –pbc nojump) and problem fixed. But now I have ano

[gmx-users] Fwd: -pbc nojump

I did simulation of protein-dna complex in water solvent. After simulation, two strands of dna was separated when I displayed my a.xtc with VMD.I used (trjconv –f a.xtc –s a.tpr –n a.ndx –o b.xtc –pbc nojump) and problem fixed. But now I have another problem. Before using –pbc nojump, there wer

[gmx-users] Fwd: Residue 'MOL' not found in residue topology database

Probably I wasn't the only one who got this in a personal mail box, but I'll forward it anyway. And, no, I'm not a private tutor, unless I've explicitly indicated otherwise. Tsjerk -- Forwarded message -- From: AJANI HARESH Date: Thu, Sep 16, 2010 at 2:00 PM Subject: Residue 'MO

[gmx-users] Fwd: Question

Please let me know the answer of this question: I can't understand it. How can this occur?(You had mentioned it in the Gromacs manual user guide(chapter 7)) Can gromacs write* conserved energy quantity* in log file when we are simulating a *NVT* ensemble? Do you mean* Kinetic energy* is conserv

[gmx-users] Fwd: PE compressing - for reference only

Dear Moeed: Please find attached the simulation results as well as the input files for your PE system. I started the simulation from your 8PE configuration and compressed it to the density of ~890 kg/m3. It is rather good since ranges between the experimental values - http://en.wikipedia.org/wiki/

[gmx-users] Fwd: dissolution of gases in liquid

In addition, we also tried to equilibrate the liquid-gas interface in the NVT and then switched on barostat. The result with barostat was unfortunately the same. I suspect the problem is in the (anisotropic) pressure coupling but I still have no idea how it can be corrected. The described setup is

Re: [gmx-users] Fwd: missing atom

Dear Abdul, I had a similar error always with residue number 2 when using the amber ports in gromacs. Manually adding the hydrogen to the backbone nitrogen that connects to residue 1 will fix this. You might know how to do this but just in case here is how I do it: load your pdb into any builder

[gmx-users] Fwd: missing atom

Dear Abdul, please keep all Gromacs-related questions on the mailing list. Best, Carsten Begin forwarded message: > From: "abdul wadood" > Date: July 3, 2010 8:40:29 AM GMT+02:00 > To: > Subject: missing atom > > Dear Carsten > > I am running simulation using gromacs with amber forcefie

[gmx-users] Fwd: how to position restraint COM of clusters?

Hi I noticed a new position restraint com function of Gromacs (Implement new position restraints that restrain particles with respect to the center of mass of a group (e.g. for cluster simulations).) How can I get detailed mdp file set up for this function? Is it a pr.mdp or md.mdp with pull code?

[gmx-users] Fwd: reproducibility of PMF plot with two different starting structures?

Hi, I just want to know about the consistency we could obtain in plotting PMF. I am using Gromacs 4.0.4 MPI version. Trying to find the PMF of the ligand transport through the channel. I tried two SMDs (same pull rate, and force constant) with different starting structures (only ligand poses and

[gmx-users] Fwd: small help

Dear Satish, you'll find more help in the mailing list of GROMACS. regarding the use of g_rmsdist, the option -h is very useful ... you can access single residues or subpart of a system by using and index. XAvier. Begin forwarded message: From: satish kumar ainala Date: April 13, 2010 12:1

Re: [gmx-users] Fwd: help

On 8/04/2010 2:22 PM, Sepideh Soltani wrote: Please send one email, not three. If you learn how to use your tools properly, you make a much better impression of being someone worth someone else's time to help. -- Forwarded message -- From: *Sepideh Soltani* mailto:sepideh.sol

[gmx-users] Fwd: moleculetype CU1+ is redefined

-- Forwarded message -- From: Sepideh Soltani Date: Thu, Apr 8, 2010 at 12:33 AM Subject: Fwd: moleculetype CU1+ is redefined To: sepideh.solt...@gmail.com Begin forwarded message: *From: *Sepideh Soltani *Date: *April 8, 2010 12:33:00 AM EDT *To: *gmx-us...@gromacs.org *Subj

[gmx-users] Fwd: help

-- Forwarded message -- From: Sepideh Soltani Date: Wed, Apr 7, 2010 at 11:21 PM Subject: help To: gmx-users-requ...@gromacs.org Hi all, I am running with gromacs 4.0.5. I am trying to do gromacs tutorial for drug-enzyme complex. I did this tutorial step by step but when I used

[gmx-users] Fwd: Deprotonated Cys

If the Cys is bound to a heme iron it should work out of the box, but only for certain force fields. from specbond.dat: CYS SG 1 CYS SG 1 0.2 CYS2CYS2 CYS SG 1 HEMEFE 2 0.25CYS2HEME CYS SG 1 HEMECAB

Re: [gmx-users] Fwd: pdb2gmx command

On 2010-03-07 12.23, bharat gupta wrote: Hi all, I have modelled a protein with one residue as formylated glycine which is the active site residue of my protein and when I am running the pdb2gmx command I am getting the following error :- Back Off! I just backed up npep.top to ./#npep.top.4# Pr

[gmx-users] Fwd: pdb2gmx command

Hi all, I have modelled a protein with one residue as formylated glycine which is the active site residue of my protein and when I am running the pdb2gmx command I am getting the following error :- Back Off! I just backed up npep.top to ./#npep.top.4# Processing chain 1 (2862 atoms, 358 residues)

[gmx-users] Fwd: md.c for 3.3.3

For the record, I wanted to point out that there is a semi-official GROMACS 3.3.4 (really, a patch) with link below. The reason this is called "3.3.4" is that I'm working with some supercomputing folks who sort of refused to install my bugfixed version of 3.3.3 site-wide unless it was an official

[gmx-users] Fwd: Help for REMD

Please keep GROMACS correspondence on the mailing list. Nobody here is a private tutor unless you're paying them. Original Message Subject: Help for REMD Date: Mon, 01 Feb 2010 14:58:08 +0200 (EET) From: Murat Erman OGUZ To: mark.abra...@anu.edu.au Dear Mr.Mark Abraham I am E

Re: [gmx-users] Fwd: xmgrace

On Sat, 2010-01-30 at 12:03 +0100, David van der Spoel wrote: > On 1/30/10 11:04 AM, bharat gupta wrote: > > Sir > > > > I am installing openMotif-2.2.3 version but after make command I > > getting the follwoing error :- > > > Why not use the redhat software: > > yum install openmotif-devel > > o

Re: [gmx-users] Fwd: xmgrace

On 1/30/10 11:04 AM, bharat gupta wrote: Sir I am installing openMotif-2.2.3 version but after make command I getting the follwoing error :- In file included from XmStrDefs.c:10: ../Xm/Xm.h:59:34: error: X11/extensions/Print.h: No such file or directory In file included from XmStrDefs.c:10: ../

Re: [gmx-users] Fwd: xmgrace

Sir I am installing openMotif-2.2.3 version but after make command I getting the follwoing error :- In file included from XmStrDefs.c:10: ../Xm/Xm.h:59:34: error: X11/extensions/Print.h: No such file or directory In file included from XmStrDefs.c:10: ../Xm/Xm.h:827: error: expected specifier-qual

Re: [gmx-users] Fwd: xmgrace

On 1/30/10 10:30 AM, bharat gupta wrote: hi all, I am trying to install xmgrace on redhat linux 5 and I am getting the following two errors after running the ./configure command :- checking for a Motif>= 1002 compatible API... no configure: error: M*tif has not been found Can u pls tell how c

[gmx-users] Fwd: xmgrace

hi all, I am trying to install xmgrace on redhat linux 5 and I am getting the following two errors after running the ./configure command :- checking for a Motif >= 1002 compatible API... no configure: error: M*tif has not been found Can u pls tell how can I rectify the error .. or shall I go fo

Re: [gmx-users] Fwd: x2top(4.0.7). More.

Justin, Thanks. The problem was that I didn't use "-nopbc" option. Vitaly On Sun, Jan 17, 2010 at 7:11 PM, Justin A. Lemkul wrote: > > > Vitaly V. Chaban wrote: >> >> And more. What is the algorithm to detect that the proper atom group? >> Is it based both on the atom names in PDB and interato

Re: [gmx-users] Fwd: x2top(4.0.7). More.

Vitaly V. Chaban wrote: And more. What is the algorithm to detect that the proper atom group? Is it based both on the atom names in PDB and interatomic distances? So if we have for example Oopls_236-0.5 15.9994 1C 0.123 and in the submitted structure r(C-O)=0.126 - what it be re

[gmx-users] Fwd: x2top(4.0.7). More.

And more. What is the algorithm to detect that the proper atom group? Is it based both on the atom names in PDB and interatomic distances? So if we have for example Oopls_236-0.5 15.9994 1C 0.123 and in the submitted structure r(C-O)=0.126 - what it be recognized? Thanks in advance

Re: [gmx-users] Fwd: What could be wrong with rdf plot?

bject: Re: [gmx-users] Fwd: What could be wrong with rdf plot? It is always better to keep the discussion in the list. Someone could benefit of it as well as you from others. From: Lum Nforbi Date: January 4, 2010 7:57:04 PM GMT+01:00 To: XAvier Periole Subject: Thank you for reply on RDF

RE: [gmx-users] Fwd: What could be wrong with rdf plot?

From: gmx-users-boun...@gromacs.org on behalf of XAvier Periole Sent: Tue 1/5/2010 6:33 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Fwd: What could be wrong with rdf plot? It is always better to keep the discussion in the list. Someone could benefit of it as well as you from o

Re: [gmx-users] Fwd: What could be wrong with rdf plot?

or you have to find out our self, looking at the code or in the archive :)) Thank you, Lum Message: 3 Date: Sun, 3 Jan 2010 13:18:29 +0100 From: XAvier Periole Subject: Re: [gmx-users] Fwd: What could be wrong with rdf plot? To: Discussion list for GROMACS users Message-ID: <28fdb30b-7

Re: [gmx-users] Fwd: mdrun error

Amir Marcovitz wrote: -- Forwarded message -- From: *Amir Marcovitz* mailto:amarcov...@gmail.com>> Date: Mon, Jan 4, 2010 at 6:18 PM Subject: mdrun error To: gmx-users-requ...@gromacs.org Hi, my system is composed of 2 molecules that

[gmx-users] Fwd: mdrun error

-- Forwarded message -- From: Amir Marcovitz Date: Mon, Jan 4, 2010 at 6:18 PM Subject: mdrun error To: gmx-users-requ...@gromacs.org Hi, my system is composed of 2 molecules that are arranged in a lattice: i.e., each molecule is represented by 4 atoms (which are charged) and o

Re: [gmx-users] Fwd: What could be wrong with rdf plot?

I am not sure somebody gave you an answer ... the first intense and probably very narrow pick is very likely due to the intramolecular OH distance. It should be around 0.1 nm, isn't it? On Jan 1, 2010, at 3:53 AM, Lum Nforbi wrote: -- Forwarded message -- From: Lum Nforbi D

[gmx-users] Fwd: What could be wrong with rdf plot?

-- Forwarded message -- From: Lum Nforbi Date: Thu, Dec 31, 2009 at 12:33 PM Subject: What could be wrong with rdf plot? To: gmx-users@gromacs.org Dear all, I am currently analyzing a system of 2000 molecules of TIP3P water on which I performed a NPT simulation. The plot fo

[gmx-users] [Fwd: Gromacs podcast is out]

For your entertainmet during the holiday season, here are links to a podcast about GROMACS' past, present and future. Brock Palen and Jeff Squyres chat with me about GROMACS. Enjoy. http://www.rce-cast.com/index.php/Podcast/rce-23-gromacs.html The RSS feed for the show is: http://www.rce-c

[gmx-users] [Fwd: installing gromacs on vista]

Hi, I am not a free private help service. Please search the GROMACS webpage first, where your question is answered. If you have a specific problem, please ask the mailing list. On point, GROMACS is a simulation package, not a molecule viewer. Mark Original Message Subject:

Re: [gmx-users] Fwd: RDF plot. This is weird!

It came through just fine for me; see my reply that I posted earlier: http://lists.gromacs.org/pipermail/gmx-users/2009-December/047358.html -Justin Lum Nforbi wrote: Hi, I am forwarding the message and the attachment because I did not see my message in the inbox of gmx-users; I saw only the

[gmx-users] Fwd: RDF plot. This is weird!

Hi, I am forwarding the message and the attachment because I did not see my message in the inbox of gmx-users; I saw only the attached file. Please, can the text be included? Thank you. -- Forwarded message -- From: Lum Nforbi Date: Wed, Dec 9, 2009 at 11:59 AM Subject: RDF plot.

Re: [gmx-users] Fwd: Last step before CG em.mdp

Justin A. Lemkul wrote: Then that's certainly the first problem to fix. This is why I generally use editconf for defining the box (and why I keep recommending it). For a simple protein in water, using a command like: editconf -c -d 1.0 will define a suitably-sized box so that you don't h

Re: [gmx-users] Fwd: Last step before CG em.mdp

Francesco Pietra wrote: On Mon, Nov 30, 2009 at 8:18 PM, Justin A. Lemkul wrote: Francesco Pietra wrote: Failed to specify that both the DPPC bilayer and the box of water are from equilibrated systems in MARTIN web, while the protein was Amber minimized (and MD) before generating the CG. I

Re: [gmx-users] Fwd: Last step before CG em.mdp

On Mon, Nov 30, 2009 at 8:18 PM, Justin A. Lemkul wrote: > > > Francesco Pietra wrote: >> >> Failed to specify that both the DPPC bilayer and the box of water are >> from equilibrated systems in MARTIN web, while the protein was Amber >> minimized (and MD) before generating the CG. >> >> I have tr

Re: [gmx-users] Fwd: Last step before CG em.mdp

Francesco Pietra wrote: Failed to specify that both the DPPC bilayer and the box of water are from equilibrated systems in MARTIN web, while the protein was Amber minimized (and MD) before generating the CG. I have tried the cg protein alone genbox -cp my.pdb -box 15 -o my.gro Again I ask

[gmx-users] Fwd: Last step before CG em.mdp

Failed to specify that both the DPPC bilayer and the box of water are from equilibrated systems in MARTIN web, while the protein was Amber minimized (and MD) before generating the CG. I have tried the cg protein alone genbox -cp my.pdb -box 15 -o my.gro grompp -f em.mdp -c my.gro -p my.top -o to

[gmx-users] Fwd: Re: Inflategro for Coarse Grained

Forwarded Message From: Thomas Schmidt Reply-To: schm...@bit.uni-bonn.de To: mishra.su...@gmail.com Subject: Re: Inflategro for Coarse Grained Date: Thu, 29 Oct 2009 13:45:02 +0100 Dear Sunny, Justin's right. The definition of the lipid-representative atom (P) is done in line

[gmx-users] [Fwd: Gromacs installation]

Please keep correspondence on the gmx-users mailing list. This issue is routine, and is covered in the current installation guide. http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions Mark Original Message Subject:Gromacs install

[gmx-users] Fwd: unit of eigenfrequency

Hi, After the g_nmeig command the mass weighted eigenfrequency is obtained.So what is the unit of this.I calculated this by GROMACS unit and it came out to be ps-1.If it is this then how to get this in general cm-i unit.Please help me.

[gmx-users] [Fwd: free energy calculation]

Original Message Subject:free energy calculation Date: Wed, 16 Sep 2009 11:34:25 -0400 From: Elio Cino To: sp...@gromacs.org Hello. Dr. van der Spoel. I have been waiting for an account to be made on gmx-users so that i can post. Until the account is made, I

Re: [gmx-users] [Fwd: Please solve my problem]

ceste...@unsl.edu.ar wrote: Hi All I have similar problem using gromacs 4.0.2. The MD simulation (5 ns) on single processor is complited in 5 days, but the same MD can`t be complited on cluster on 4 or 8 processors. The MD simulation is stopped without any error message. If there actually is no

Re: [gmx-users] [Fwd: Please solve my problem]

Hi again the MPI coding is OPEN MPI 1.2.7 that is found in the ROCKS CLUSTER 5.1 distribution thanks Carmen > > ceste...@unsl.edu.ar wrote: >> Hi All >> I have similar problem using gromacs 4.0.2. >> The MD simulation (5 ns) on single processor is complited in 5 days, but >> the same MD can`t be c

Re: [gmx-users] [Fwd: Please solve my problem]

ceste...@unsl.edu.ar wrote: Hi All I have similar problem using gromacs 4.0.2. The MD simulation (5 ns) on single processor is complited in 5 days, but the same MD can`t be complited on cluster on 4 or 8 processors. The MD simulation is stopped without any error message. Any help would be appre

Re: [gmx-users] [Fwd: Please solve my problem]

Hi All I have similar problem using gromacs 4.0.2. The MD simulation (5 ns) on single processor is complited in 5 days, but the same MD can`t be complited on cluster on 4 or 8 processors. The MD simulation is stopped without any error message. Any help would be appreciated Carmen > > To, >D

[gmx-users] [Fwd: Please solve my problem]

To, David van der Spoel Dear Sir, I am using Gromacs 3.2.1 for the MD simulation on clusters but facing a problem. I am giving job for 50 steps step size 0.002ps (total 1ns) but my job is stopped after 47 steps. when i run this on 4 processors. But the same job is completed on 2

Re: [gmx-users] Fwd: xdrfile library, read co-ordinates from .xtc

On Tue, 2009-08-11 at 23:22 +0300, Vitaly V. Chaban wrote: > On the same topic, I have a question to the community: does anybody > try to make *so*-library (or *dll* on windows) of xdrfile in order to > use with other programming languages? I spent a day trying to master > this art but didn't still

[gmx-users] Fwd: xdrfile library, read co-ordinates from .xtc

On the same topic, I have a question to the community: does anybody try to make *so*-library (or *dll* on windows) of xdrfile in order to use with other programming languages? I spent a day trying to master this art but didn't still succeed. If somebody more experienced with dynamic libraries than

[gmx-users] Fwd: Error in PDB2GMX

Sunny, It is improper to send (un)personal mails like this, targeted to several people, just changing the addressing. Basically you qualify for straightforward neglect. Do you really think the user list is only kept for fun? And I'm not even sure I ever answered one mail related to CG simulations!

[gmx-users] Fwd: help-how to define a new residue in gromacs ?

This is what the GMX user list is for. Please post such requests there. Tsjerk -- Forwarded message -- From: 郭建路 Date: 2009/8/4 Subject: help-how to define a new residue in gromacs ? To: tsjerkw HI Tsjerk: can you help me ? My problem is How to define new residue in GROMACS?

[gmx-users] Fwd: fixed "3.3.3"?

All, Is there any chance of getting an "official" patch released for 3.3.3 that fixes the mdrun bug I have pointed out in the past, or perhaps an official, super-minor point release? I can provide the patch -- I'd just like it posted somewhere official. The reason for this is that I'm try

[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

[gmx-users] Fwd: problem with FES4 cluster

Subarna, I am not a helpdesk or mailing list, if I had had the answer, I would have replied on the mailing list already. Then, if you feel it is appropriate to send a mail to someone you don't know, at least take the effort to write a complete message. Tsjerk -- Forwarded message --

Re: [gmx-users] Fwd: Segmentation fault while running gromacs 4.0.4

Ms. Aswathy S wrote: Dept. Biotechnology Ext. 3108 - Forwarded Message - From: "Ms. Aswathy S" To: gmx-users@gromacs.org Sent: Tuesday, June 2, 2009 11:54:56 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Segmentation fault while running gromacs 4.0.4 Hi, I am working in

[gmx-users] Fwd: Segmentation fault while running gromacs 4.0.4

Dept. Biotechnology Ext. 3108 - Forwarded Message - From: "Ms. Aswathy S" To: gmx-users@gromacs.org Sent: Tuesday, June 2, 2009 11:54:56 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: Segmentation fault while running gromacs 4.0.4 Hi, I am working in GROMACS 4.0.4 and try

[gmx-users] Fwd: No plot found running .xvg files using xmgrace produced by g_helix.

-- Forwarded message -- From: Chitrita Dutta Roy Date: Mon, Mar 30, 2009 at 9:42 PM Subject: No plot found running .xvg files using xmgrace produced by g_helix. To: gmx-users Dear gromacs user, I am stuck in a problem with g_helix command. The output of the g_helix is and a s

RE: [gmx-users] [Fwd: Problems in pulling a molecule from the membrane]

guess you should use only one of the two options. Berk Date: Fri, 27 Mar 2009 14:43:48 +0100 From: schl...@uni-mainz.de To: gmx-users@gromacs.org Subject: [gmx-users] [Fwd: Problems in pulling a molecule from the membrane] I have tested the pulling in GROMACS 4.0.2 only once and there only

[gmx-users] [Fwd: Problems in pulling a molecule from the membrane]

I have tested the pulling in GROMACS 4.0.2 only once and there only with 'pull_geometry = position'. But i think the problem lies in the pressure-coupling or something which is connected to it ' Step 1 Warning: pressure scaling more than 1%, mu: 1.00054 1.00054 0.83511'. Because i have not yet use

[gmx-users] Fwd: using oplsaa in Gromacs

I refuse to act as a mailing-list subsitute. And there are others better fit to point you to: http://www.catb.org/~esr/faqs/smart-questions.html http://wiki.gromacs.org/index.php/Parameterization Tsjerk -- Forwarded message -- From: oguz gurbulak Date: Sun, Mar 15, 2009 at 2:50

[gmx-users] Fwd: Matching atom name and types in OPLS-aa FF

Since I cannot see my message on the gmx-users mail list, I am forwarding this again.I am sorry to bother your email box again... Hope you would understand... -- Forwarded message -- From: Tree Date: Fri, Mar 13, 2009 at 8:51 PM Subject: Matching atom name and types in OPLS-aa FF

Re: [gmx-users] Fwd: Force Field - Gromos96

Hi C Kim, The GROMOS96 force _is_ a united atom force field. Cheers, Tsjerk On Fri, Mar 13, 2009 at 5:30 AM, Tree wrote: > > > -- Forwarded message -- > From: tree > Date: Thu, Mar 12, 2009 at 10:09 PM > Subject: Force Field - Gromos96 > To: gmx-users@gromacs.org > > > Dear Al

[gmx-users] Fwd: Force Field - Gromos96

-- Forwarded message -- From: tree Date: Thu, Mar 12, 2009 at 10:09 PM Subject: Force Field - Gromos96 To: gmx-users@gromacs.org Dear All: I appreciate it if it would be possible for me to have an answer related to Gromos96 force field. I am hoping to know if the Gromos96 forc

[gmx-users] Fwd: How to define "stretch" in ffoplsaabon.itp ?

In the section [3], the file is "csoplsaanb.itp". In the file, I found how an opls_xxx is assigned to an atom type. (If this is a CORRECT approach...) Thank you! Sincerely, C. Kim -- Forwarded message -- From: Tree Date: Wed, Mar 4, 2009 at 9:38 AM Subject: How to define "stret

[gmx-users] Fwd: Polyethylene (PE) simulations in Gromacs - please!

-- Forwarded message -- From: Chansoo Kim Date: Tue, Mar 3, 2009 at 8:28 AM Subject: Polyethylene (PE) simulations in Gromacs - please! To: gmx-users@gromacs.org Dear Dr. Benkova and others: I am C. Kim and trying to simulation polymer system. Since I guessed that polyethylene

Re: [gmx-users] [Fwd: question about the torsional potential]

Dear David Thank you very much for your answer, but I'm interested to know what formula has been used in the case of the torsional potential: 1) V(fi) = k*(1+cos(n*fi-fi0)) or 2) V(fi) = k(1+cos(delta)*cos(n*fi)) If you do not knows this detail of the program. Could yo say me someone who

Re: [gmx-users] [Fwd: question about the torsional potential]

David van der Spoel wrote: I'm very new in the world of gromacs, but I have experience in simulation (Molecular Dynamics, Monte Carlo, Langevin Dynamics, etc) always using my own programs. Now I am starting a research in polyaniline (PANI) using GROMACS with a model potential that has been dedu

[gmx-users] [Fwd: question about the torsional potential]

I'm very new in the world of gromacs, but I have experience in simulation (Molecular Dynamics, Monte Carlo, Langevin Dynamics, etc) always using my own programs. Now I am starting a research in polyaniline (PANI) using GROMACS with a model potential that has been deduced from fisrt principles by

Re: [gmx-users] Fwd: Re[2]: gmx-users Digest, Vol 56, Issue 44

Vitaly Chaban wrote: To be complete, I compiled the mpi version via: ./configure --enable-mpi -enable-float --prefix=/{PATH}/gmx402 -program-suffix="_mpi" make make install Was anything missed, perhaps? configure should have complained because two of those options are not correctly formatted

Re: [gmx-users] Fwd: Re[2]: gmx-users Digest, Vol 56, Issue 44

Vitaly Chaban wrote: To be complete, I compiled the mpi version via: ./configure --enable-mpi -enable-float --prefix=/{PATH}/gmx402 -program-suffix="_mpi" make make install Was anything missed, perhaps? Which MPI are you using? You might also try to recreate your tpr file. Vitaly ===8<===

[gmx-users] Fwd: Re[2]: gmx-users Digest, Vol 56, Issue 44

To be complete, I compiled the mpi version via: ./configure --enable-mpi -enable-float --prefix=/{PATH}/gmx402 -program-suffix="_mpi" make make install Was anything missed, perhaps? Vitaly ===8<==Original message text=== Unfortunately, the upgrade to 4.0.2 did not help.

Re: [gmx-users] [Fwd: Loss of bonds in HEME iron after pdb2gmx]

Dear Sarada, You need to paramterize the Cysteinyl ligand manually. There are a variety of references in the literature that provide reasonable energies. Below is a pretty good reference. Best wishes, Art 1. Oda, A., Yamaotsu, N., and Hirono, S. (2005) New AMBER force field parameters o

[gmx-users] [Fwd: Loss of bonds in HEME iron after pdb2gmx]

Hello, I am working with the simulation of cytochromeP450. There is a bond between the S of cystine and FE of HEME. During the grompp step I get warnings that there is no default bonds/angles/dihedrals all pertaining to the cystine-heme bond. In the archives it was mentioned that these values must

Re: [gmx-users] [Fwd: [FFTW-announce] FFTW 3.2 is released]

On Nov 16, 2008, at 12:47 PM, Mark Abraham wrote: Apologies to people receiving this from the FFTW list too, but it should be of interest to a large slice of people using GROMACS. In particular, the improvements for SIMD and size of multiples of 5/10 should be of value for lots of people.

[gmx-users] [Fwd: [FFTW-announce] FFTW 3.2 is released]

Apologies to people receiving this from the FFTW list too, but it should be of interest to a large slice of people using GROMACS. In particular, the improvements for SIMD and size of multiples of 5/10 should be of value for lots of people. Does anyone (Carsten?) have an off-the-cuff opinion on

[gmx-users] [Fwd: Water model => amber port to gromacs ? => OR]

Original Message Subject: Water model => amber port to gromacs ? => OR Date: Mon, 10 Nov 2008 01:22:07 -0800 From: Chih-Ying Lin <[EMAIL PROTECTED]> To: [EMAIL PROTECTED] CC: gmx-users@gromacs.org HI The thing is the definition of atom type, OW and H in gromos 96 are different f

Re: [gmx-users] Fwd: still problem with lamboot

So for the two cores on your notebook it works? If you can get an answer from the remote host by using e.g. "ping remotehost" then lamboot should in principle also work. If it does not, carefully read the error message that comes from lam. It could be that there is some output on stderr coming fro

[gmx-users] Fwd: still problem with lamboot

  Note: Forwarded message attached -- Original Message -- From: "sarbani chattopadhyay" <[EMAIL PROTECTED]> To: "gmx_usrs" <[EMAIL PROTECTED]> Subject: still problem with lamboot --- Begin Message ---  Dear Carsten, Thanks for your reply. As per your suggestion I tried

[gmx-users] Fwd: The question from the tutorial: Add water spc216.gro

Hi Lin, This is also gromacs related, rather than tutorial related. You followed the tutorial and now went off to try the procedures on your own system. As for the question, searching the user list with "settles" and "bounds" gives me the following: http://www.gromacs.org/pipermail/gmx-users/2007

[gmx-users] Fwd: The question from the tutorial: protein non-protein in .mdp file

Hi Lin, Better keep this discussion on the list now. Sorry about the link. Got screwed up. It should only consist of the first part: http://wiki.gromacs.org/index.php/Thermostats Then, if you don't have protein in the first place, you can't rely on standard groups. You'll have to work with an ind

[gmx-users] [Fwd: Problem in running energy minimization in gromacs]

Original Message Subject: Problem in running energy minimization in gromacs Date: Mon, 27 Oct 2008 15:16:23 + From: abhik mukhopadhyay <[EMAIL PROTECTED]> To: [EMAIL PROTECTED] Dear Dr. Spoel Good day. I am a beginner in Gromacs and having some problem in running energy m

[gmx-users] Fwd: gromacs

-- Forwarded message -- From: He, Yang <[EMAIL PROTECTED]> Date: Mon, Oct 13, 2008 at 5:35 PM Subject: gromacs To: "[EMAIL PROTECTED]" <[EMAIL PROTECTED]> Hi , I am using the gromcas to simulate the course grain for DNA. I listed the new atom types in the .atp file like this Ab

[gmx-users] Fwd: force field for boron-nitride nanotube

Dear all user How can I have a force field for simulation of boron-nitride nanotube? The pdb file of nanotube is as follow: HETATM1 N1 UNK 1 1.597 0.000 -5.015 1.00 0.00 N HETATM2 N2 UNK 1 1.129 1.129 -2.870 1.00 0.00 N HETATM3 B3 UNK 1 1

Re: [gmx-users] Fwd: charges,resonance and electrostatics

Omer Markovitch wrote: There is no non-bonded interaction between these two oxygens, unless you are using an Urey-Bradley potential for the angle, like in the CHARMM force field. Most (if not all) of the standard force fields in Gromacs treat the interaction of

Re: [gmx-users] Fwd: charges,resonance and electrostatics

> > >> There is no non-bonded interaction between these two oxygens, unless you >> are using an Urey-Bradley potential for the angle, like in the CHARMM force >> field. Most (if not all) of the standard force fields in Gromacs treat the >> interaction of these oxygens within an angle definition, wh

Re: [gmx-users] Fwd: charges,resonance and electrostatics

Omer Markovitch wrote: Hello, There is a point, I want to clear out for myself: Say we focus on the aspartate residue. It has a formal charge of -1. This charge on either oxygen of the carboxyl is -0.8 (oxygens OD1 & OD2), according to one of the force fields employed in GROMACS. What is the

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