[gmx-users] DFLEXIBLE parameter

Dear all gmx users and developers, Parameter -DFLEXIBLE in mdp file will include flexible water in stead of rigid water into the topology. So, will it affect the MD simulation if I include this parameter in the MD simulation? because it is unnecessary in the run parameter. Any comments and s

[gmx-users] Is it the correct label on Y axis ( density graph)

Dear all, I am wondering that is it the correct label of y axis in the density graph which i obtained using g_energy? because it is not a density unit but is labeled as kJ/mol Thanks guys. ___ gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] density graph ( density vs time)

ty graph ( density vs time) > To: [EMAIL PROTECTED], "Discussion list for GROMACS users" > > Date: Tuesday, October 28, 2008, 11:31 PM > huan wrote: > > Dear all, > > > > Previously i obtained a density (y-axis) versus box > length (x axis) using g_

Re: [gmx-users] density graph ( density vs time)

TED]> wrote: > From: Mark Abraham <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] density graph ( density vs time) > To: "Discussion list for GROMACS users" > Date: Tuesday, October 28, 2008, 4:46 PM > huan wrote: > > Dear all gmx-users and developers.

[gmx-users] density graph ( density vs time)

Dear all gmx-users and developers. I wish to get a density graph with density versus time instead of nm, so how can i obtained this? Thanks. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] differentiate color of molecules

Dear all gms-users and developers, I have 6 types of molecules in my system. So, when i view the pdb file (results) using Rasmol, i cannot differentiate the molecules by their colors. Any suggestions for me to have a better way to differentiate the molecules? Thanks __

[gmx-users] workshop

Dear all. What is the procedure if we ( my research group) want to organize a workshop at my University? Thanks ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] density graph 2

Dear all Gmx users and developers, How can i get a density graph with x-axis is time scale? I obtained a density graph using g_density which output a graph with density vs nm (box size). So how can i get a graph with density vs time? Thanks _

Re: [gmx-users] density graph

density graph > To: [EMAIL PROTECTED], "Discussion list for GROMACS users" > > Date: Wednesday, October 15, 2008, 9:07 AM > huan wrote: > > Dear all gmx users and developers, > > Is it correct that in gromacs energy (density graph), > the y-axis is labell

[gmx-users] density graph

Dear all gmx users and developers, Is it correct that in gromacs energy (density graph), the y-axis is labelled as kJ/mol, I am wonder it is not a density unit. Thanks ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.o

[gmx-users] backup .xtc and .trr

Dear all gmx users and developers, I am facing a problem to copy .trr and .xtc file to my external hard disk. I need to copy these files in order to back up them. .trr file is about 10.6 Gb and .xtc file is about 7Gb. I tried to zip the files but still do not work. any suggestions are appreciat

[gmx-users] g_energy

Dear all gmx users and developers, I selected the option 1, which is BOND in g_energy analyzation. I was then obtain a graph of bond energy (the graph is similar to potential energy graph). So, i am wonder what is the meaning of the graph? Another question is: what can we obtain or explain by t

[gmx-users] Marrink et al paper

Dear all, I have read through the journal which David suggested. So,I am wonder how to generate the graph that show the comparison of the stability of cylindrical and sperical micell ( as stated as Figure 2 in that paper) Thanks. --- On Tue, 9/23/08, David van der Spoel <[EMAIL PROTECTED]

[gmx-users] XTC error

Dear gmx developers and users. I was trying to extend my simulation using tpbconv, and then mdrun. Unfortunately, my simulation crash in the half way. it stated there" XTC error". The command i used was: tpbconv -s p1.tpr -f p1.trr -e p1.edr -n p1.ndx -extend 5000 -until 1 -o extend.tpr

Re: [gmx-users] colour of the molecules

IL PROTECTED]> > Subject: Re: [gmx-users] colour of the molecules > To: [EMAIL PROTECTED], "Discussion list for GROMACS users" > > Date: Wednesday, August 13, 2008, 2:28 PM > Hi, > > On Wednesday, 13. August 2008, huan wrote: > > Dear all gmx-users a

[gmx-users] colour of the molecules

Dear all gmx-users and developers, There are 6 different type of molecules in my simulation system. So how can I differentiate o recognize the type of those molecules? which files (topology, trr or others) should I look at? Any suggestions are appreciated. Thanks

[gmx-users] Re: segmentation fault during MD and develop parameter

ameters for an alkane CH2 group (opls_136) to > your atom in > question? > > Just an idea, but I have no idea if this is a unique > situation that > requires unique parameter development. > > -Justin > > huan wrote: > > Dear all Gmx users n deve

[gmx-users] segmentation fault during MD and develop parameter

--- On Fri, 7/4/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > From: Justin A. Lemkul <[EMAIL PROTECTED]> > Subject: [gmx-users] Re: segmentation fault during MD and develop parameter > To: "Gromacs Users' List" > Date: Friday, July 4, 2008, 10:13 PM >

[gmx-users] segmentation fault during MD and develop parameter

Justin A. Lemkul <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] segmentation fault during MD > To: [EMAIL PROTECTED], "Discussion list for GROMACS users" > > Date: Friday, July 4, 2008, 6:41 PM > huan wrote: > > Dear gmx users and developers. > > >

[gmx-users] segmentation fault during MD

Dear gmx users and developers. I was running a simulation with 5 ns. But it stated "segmentation fault" at time around 1 ns, and the simulation was stopped. By the way, i faced 2 warning during running the Grompp, it stated there:" warning 1 No default Ryckaert-Bell types, using zeroes"

[gmx-users] segmentation fault during MD

Dear gmx users n developers. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe reques

[gmx-users] force field

Dear all gmx users and developers, I am running a simulation of esters. However,i failed to allocate the force field of 1 of the Carbons. (I am using OPLS-AA force field) -C-C=C-C-C=C-C- * The Carbon atom labeled with symbol * cannot be identified. I checked the ffoplsaa.atp file but I

[gmx-users] To obtain a pdb file

Hi gmx users and developers. I am wonder is there any other program or server which can use to obtain a pdb file? Currently i am using the Dundee Pro Drg Server. I am looking for other program or server. Thanks. ___ gmx-users mailing listgm

[gmx-users] unsolved topology problems.

Dear all gmx users and developers, The structure of mine is: C-C-C-C-C-C-C-C-C=C-C-C-C-C-C-C-C-C-O | C-C-C-C-C-C=C-C-C=C-C-C-C-C-C-C-C-C=O # # * # # I use opls_142 for the carbon labeled with s

[gmx-users] unsolved topology problems.

Dear all gmx users and developers, The structure of mine is: C-C-C-C-C-C-C-C-C=C-C-C-C-C-C-C-C-C-O | C-C-C-C-C-C=C-C-C=C-C-C-C-C-C-C-C-C=O # # * # # I use opls_142 for the carbon labeled with s

Re: [gmx-users] error in topology file

wrote: > huan wrote: > > Dear all gmx users and developers, > > > > After i run the grompp, there were two warnings > > appeared. The warning statements are as follow: > > > > warning 1 [File "p1.top" line 208] > > No default Ryc

[gmx-users] how to obtain no. of aggregates vs time graph

hello gromacs users.. i had read a journal which used Gromacs program in the project. I am wondering how to obtain the number of aggregates vs time graph and the size distribution of aggregates graph?? thanks for the help. __

[gmx-users] (no subject)

hello gromacs users.. i had read a journal which used Gromacs program in the project. I am wondering how to obtain the number of aggregates vs time graph and the size distribution of aggregates graph?? thanks for the help. _

[gmx-users] not center..

i found that the molecules are not at the center of the box everytimes after the simulation..they always appear at a side of the box..izzit it is related with the energy minimization? thankz Be a better pe

[gmx-users] out from the simulation box

i am doing simulation on wax ester, i am wonder why my esters sometimes are out from my simulation box at the end of the simulation? my box is cubic and 5nm x 5nm x 5nm in size. thanks. scot. Get easy, o

Re: [gmx-users] problems with opls_

i checked it but the what is the atomtype for opls_064 for? thanks --- David van der Spoel <[EMAIL PROTECTED]> wrote: > huan wrote: > > i am a new user of Gromacs and i would like to > knoe > > the opls for C, =O, and -O in RCOOR'. i tried it > many >

[gmx-users] problems with opls_

i am a new user of Gromacs and i would like to knoe the opls for C, =O, and -O in RCOOR'. i tried it many times but i still fail to get the proper answer.. thanks __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around htt