Re: [gmx-users] running a crashed run

On 01/20/11, bharat gupta wrote: > I have read that document .. but still I do have confusion .. > >   > > mdrun -s md_0_1.tpr -f md_0_1.trr -e md_0_1.edr -o md_0_1.trr -g md_0_1.log > -cpi -append... and I also completed 2 ns of the 3ns simulation.. So I want > to whether it will start fro

[gmx-users] Re: gmx-users Digest, Vol 81, Issue 126

> Message: 5 > Date: Wed, 19 Jan 2011 08:37:20 -0500 > From: "Justin A. Lemkul" > Subject: Re: [gmx-users] Re: Problem in Disulfide Bond > To: Discussion list for GROMACS users > Message-ID: <4d36e910.6030...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > parthi...@

[gmx-users] Re: Problem in Disulfide Bond

> Message: 5 > Date: Wed, 19 Jan 2011 08:37:20 -0500 > From: "Justin A. Lemkul" > Subject: Re: [gmx-users] Re: Problem in Disulfide Bond > To: Discussion list for GROMACS users > Message-ID: <4d36e910.6030...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > parthi...@

[gmx-users] glycam amber in gromacs mixed 1-4 scaling glycam06 fudgeQQ pairs coulomb amberports

Hi all, I currently mix GLYCAM and AMBER in gromacs4.0.7 using the amberports and amb2gmx.pl for the glycan. My problem is that I can't mix the scaling properly as required for correct rotamer population sampling of the glycan with the protein present. >From Glycam_06g.dat: "Correct rotational be

Re: [gmx-users] Re: Problem in Disulfide Bond

Show us that part of your topology. When you used ffamberports have you renamed the CYS to CYS2? Oliver On 20 January 2011 09:23, wrote: > > Message: 5 > > Date: Wed, 19 Jan 2011 08:37:20 -0500 > > From: "Justin A. Lemkul" > > Subject: Re: [gmx-users] Re: Problem in Disulfide Bond > > To: Disc

Re: [gmx-users] Re: Problem in Disulfide Bond

On 01/20/11, parthi...@ncbs.res.in wrote: > > Message: 5 > > Date: Wed, 19 Jan 2011 08:37:20 -0500 > > From: "Justin A. Lemkul" > > Subject: Re: [gmx-users] Re: Problem in Disulfide Bond > > To: Discussion list for GROMACS users > > Message-ID: <4d36e910.6030...@vt.edu> > > Content-Type: text/p

[gmx-users] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3

Hi I have a protein whose topology I built using pdb2gmx with the -ss option and the opls-aa force field. When I run grompp, the total charge on the protein is reported as 2.9 (not 2.999). Why a non-zero charge? Does this have something to do with the disulfide bridge? Secondly, when I run a simu

Re: [gmx-users] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3

On 01/20/11, maria goranovic wrote: > Hi > > I have a protein whose topology I built using pdb2gmx with the -ss option and > the opls-aa force field. When I run grompp, the total charge on the protein > is reported as 2.9 (not 2.999). Why a non-zero charge? Does this have > something to do

Re: [gmx-users] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3

Hi I have figured out the vacuum slow problem. It turns out I was using PBC in vacuum with PME. It is now fixed. The other problem is still there. My protein has 2 chains. one chain is simply a glutamate residue. Its charge (both terminii charged is -1.11 instead of -1). here is the section of th

[gmx-users] Mesa GLproto stuff UBUNTU

Hello, I am wondering if anyone has had luck installing glproto for a functional Mesa package on Ubuntu? Thing is I am trying to install wxmacmolplt-7.4.2 to view QM/MM results, but get nowhere without a functional Open GL emulator. Thanks Sergio -- gmx-users mailing listgmx-users@gromacs.or

Re: [gmx-users] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3

maria goranovic wrote: Hi I have figured out the vacuum slow problem. It turns out I was using PBC in vacuum with PME. It is now fixed. The other problem is still there. My protein has 2 chains. one chain is simply a glutamate residue. Its charge (both terminii charged is -1.11 instead of

[gmx-users] avoiding bad contact in continutation run

Dear gmx-users, I am simulating a dppc + chol system, the force field is martini with gromacs 3.3.3 the system was initially run for 150 ns, but i had to later extend the simulation, so using the confout.gro and with mdp options: gen_vel = no unconstrained_start = yes I gave a re-run fo

[gmx-users] Re: Problem in Disulfide Bond

> Message: 3 > Date: Thu, 20 Jan 2011 09:30:00 + > From: Oliver Grant > Subject: Re: [gmx-users] Re: Problem in Disulfide Bond > To: Discussion list for GROMACS users > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Show us that part of your topology. When you used

Re: [gmx-users] Re: Problem in Disulfide Bond

parthi...@ncbs.res.in wrote: Message: 3 Date: Thu, 20 Jan 2011 09:30:00 + From: Oliver Grant Subject: Re: [gmx-users] Re: Problem in Disulfide Bond To: Discussion list for GROMACS users Message-ID: Content-Type: text/plain; charset="iso-8859-1" Show us that part of your topology

Re: [gmx-users] Re: Problem in Disulfide Bond

On 01/20/11, parthi...@ncbs.res.in wrote: > > Message: 3 > > Date: Thu, 20 Jan 2011 09:30:00 + > > From: Oliver Grant > > Subject: Re: [gmx-users] Re: Problem in Disulfide Bond > > To: Discussion list for GROMACS users > > Message-ID: > >  > > Content-Type: text/plain; charset="iso-8859

[gmx-users] 4 x Opteron 12-core or 4 x Xeon 8-core ?

Dear Gromacs Users, We're going to buy a new server for HPC. It is going to run mainly Gromacs calculations. Regarding Gromacs performance, I'm wondering which one, you Gromacs users and developers, think will be faster. AMD Server : 4 x AMD Opteron 6176 12-core 2.3 Ghz + 96GB Memory

Re: [gmx-users] avoiding bad contact in continutation run

On 01/20/11, Adwait Mevada wrote: > >  Dear gmx-users, >  I am simulating a dppc + chol system, the force field is martini with > gromacs 3.3.3 the system was initially run for 150 ns, but i had to later > extend the simulation, so using the confout.gro and with mdp options: > gen_vel = no >

Re: [gmx-users] 4 x Opteron 12-core or 4 x Xeon 8-core ?

Hi David, On Jan 20, 2011, at 1:21 PM, David McGiven wrote: > Dear Gromacs Users, > > We're going to buy a new server for HPC. It is going to run mainly Gromacs > calculations. > > Regarding Gromacs performance, I'm wondering which one, you Gromacs users and > developers, think will be faster

Re: [gmx-users] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3

I did use -ter and chose -COO and NH3+. Am i supposed to chose Zwitterion_COO- and Zwitterion_NH3+ ? On Thu, Jan 20, 2011 at 12:55 PM, Justin A. Lemkul wrote: > > > maria goranovic wrote: > >> Hi >> >> I have figured out the vacuum slow problem. It turns out I was using PBC >> in vacuum with PME

Re: [gmx-users] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3

maria goranovic wrote: I did use -ter and chose -COO and NH3+. Am i supposed to chose Zwitterion_COO- and Zwitterion_NH3+ ? That's what I said, and that's what you have, isn't it? A single amino acid that should have both its termini charged? -Justin On Thu, Jan 20, 2011 at 12:55 PM, J

[gmx-users] Re: avoiding bad contact in continutation run (Mark Abraham)

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Re: [gmx-users] QM/MM viewer (was: CNT)

As much as I appreciate being seen as a reliable source of information, I have no experience with this program and no time to investigate it on my own. Please remember a few things: First, please do not hijack someone else's thread to ask an unrelated question. Second, this is a forum for G

Re: [gmx-users] Re: avoiding bad contact in continutation run (Mark Abraham)

.gromacs.org/Support/Mailing_Lists -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110120/3f5c3a23/attachment.html -- -- gmx-users mailing list gmx-users@gromacs.org http://list

[gmx-users] QM/MM viewer

Does anyone know of a free-of-charge viewer for QM/MM results from G03, for Ubuntu? It should be able to show electron orbitals, polarizabilities, bond strength etc. Sergio -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the arc

Re: [gmx-users] Re: Problem in Disulfide Bond

In the pdb, before pdb2gmx, rename the CYS residues involved in the S-S bonds as CYS2. If you don't know this then you need to read everything on this page about using the amberports: http://ffamber.cnsm.csulb.edu/ As you may have other issues with HIS and LYS residues. Oliver -- gmx-users mailin

[gmx-users] different versions- different output!

Hello all, I am a little confused since I am not getting the same output from the same input files using two different versions (the most recent one: 4.5.3 and 4.0.7). I am using two different machines and size of data generated from these simulations are not the same either. Below is the output o

Re: [gmx-users] 4 x Opteron 12-core or 4 x Xeon 8-core ?

Dear Carsten, Thanks for the advice! The thing is that considering the price differences, we could buy 2-3 AMD machines (48 core) for each 1 Intel machine (32) core. I'm only curious about how much faster Intel will be. Side to side, amd 48core vs intel 32core, would make us talk about 2x

RE: [gmx-users] 4 x Opteron 12-core or 4 x Xeon 8-core ?

Hi, For systems or your size, they should run about equally fast. Berk > From: davidmcgiv...@gmail.com > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] 4 x Opteron 12-core or 4 x Xeon 8-core ? > Date: Thu, 20 Jan 2011 14:39:14 +0100 > > Dear Carsten, > > Thanks for the advice! > > The

[gmx-users] How to install a new Forcefield in Gromacs 4.5.3

Dear all, I would like to try a new forcefield in Gromacs 4.5.3. What should I do after I copied the ff to /share/gromacs/top directory? It seems the original FF.dat doesn't exist in 4.5.3.. Could you give me some help? Best, Qin -- gmx-users mailing listgmx-users@gromacs.org http://lists.g

Re: [gmx-users] How to install a new Forcefield in Gromacs 4.5.3

Qin Qiao wrote: Dear all, I would like to try a new forcefield in Gromacs 4.5.3. What should I do after I copied the ff to /share/gromacs/top directory? It seems the original FF.dat doesn't exist in 4.5.3.. Could you give me some help? pdb2gmx detects forcefield directories by searching

[gmx-users] Re: gmx-users Digest, Vol 81, Issue 140

1. Re: avoiding bad contact in continutation run (Mark Abraham) Adwait Mevada wrote: On 01/20/11, Adwait Mevada wrote: Dear gmx-users, I am simulating a dppc + chol system, the force field is martini with gromacs 3.3.3 the system was initially run for 150 ns, but i had to later e

Re: [gmx-users] avoiding bad contact in continutation run

Adwait Mevada wrote: 1. Re: avoiding bad contact in continutation run (MarkAbraham) Adwait Mevada wrote: On 01/20/11, Adwait Mevada wrote: Dear gmx-users, I am simulating a dppc + chol system, the force field is martini with gromacs 3.3.3 the system was initially run for 150 ns,

Re: [gmx-users] How to install a new Forcefield in Gromacs 4.5.3

2011/1/20 Justin A. Lemkul > > > Qin Qiao wrote: > >> Dear all, >> >> I would like to try a new forcefield in Gromacs 4.5.3. What should I do >> after I copied the ff to /share/gromacs/top directory? It seems the original >> FF.dat doesn't exist in 4.5.3.. Could you give me some help? >> >> > pdb

Re: [gmx-users] How to install a new Forcefield in Gromacs 4.5.3

Qin Qiao wrote: 2011/1/20 Justin A. Lemkul mailto:jalem...@vt.edu>> Qin Qiao wrote: Dear all, I would like to try a new forcefield in Gromacs 4.5.3. What should I do after I copied the ff to /share/gromacs/top directory? It seems the original FF.dat do

[gmx-users] Fwd: Viewing results from Groamcs QM/MM sims

Hi everyone, Does anyone have a suggestion for a free program to view QM/MM results from Gromacs? Thanks "The HiJacker" a.ka. S -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/M

Re: [gmx-users] How to install a new Forcefield in Gromacs 4.5.3

2011/1/20 Justin A. Lemkul > > > Qin Qiao wrote: > >> >> >> 2011/1/20 Justin A. Lemkul mailto:jalem...@vt.edu>> >> >> >> >> >>Qin Qiao wrote: >> >>Dear all, >> >>I would like to try a new forcefield in Gromacs 4.5.3. What >>should I do after I copied the ff to /share/g

Re: [gmx-users] How to install a new Forcefield in Gromacs 4.5.3

Qin Qiao wrote: 2011/1/20 Justin A. Lemkul mailto:jalem...@vt.edu>> Qin Qiao wrote: 2011/1/20 Justin A. Lemkul mailto:jalem...@vt.edu> >> Qin Qiao wrote: Dear all, I would

[gmx-users] How to create an rtp file for a lipid?

Dear All: I am trying to build a lipid bilayer made of DMPC (Dimyristoylphosphatidylcholine) surrounding a putative membrane channel. Everything goes well until I come across with the use of pdb2gmx and further on to the use of gromp, where I realized that I need to add some information about

Re: [gmx-users] How to create an rtp file for a lipid?

Dr. Ramón Garduño-Juárez wrote: Dear All: I am trying to build a lipid bilayer made of DMPC (Dimyristoylphosphatidylcholine) surrounding a putative membrane channel. Everything goes well until I come across with the use of pdb2gmx and further on to the use of gromp, where I realized that

[gmx-users] Box size and potential energy calculation

Hi, I currently read through the GMX manual 4.5.3. I have two questions: 1) Density is calculated by the density of the material and the box volume. But I can't find a reference on how the box size is calculated. Can you point me to some literature? 2) I wanted to look up the calculation of the

[gmx-users] (no subject)

Dear users, How can we fix the position of some atoms? best wishes trevor -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)

Re: [gmx-users] (no subject)

trevor brown wrote: Dear users, How can we fix the position of some atoms? Use position restraints or freeze groups. -Justin best wishes trevor -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Bioc

[gmx-users] Inaccurate pressure readings

I am running a variety of NPT simulations with polar, non-polar, and ionic compounds. Although my results for density agree well with experimental values, the pressures I get from g_energy are off by 1 to 3 orders of magnitude. In the log file, the pressure fluctuates around a lot from -400 to 40

Re: [gmx-users] Inaccurate pressure readings

Denny Frost wrote: I am running a variety of NPT simulations with polar, non-polar, and ionic compounds. Although my results for density agree well with experimental values, the pressures I get from g_energy are off by 1 to 3 orders of magnitude. In the log file, the pressure fluctuates aro

RE: [gmx-users] Inaccurate pressure readings

You have a variable that is fluctuating over a range of 800+ units (three orders of magnitude) and want the average to be 1.0? It is not a problem as such. If you can get a large enough data set of pressure data, and it will have to be very large, then you might get it close to one. But as

Re: [gmx-users] Inaccurate pressure readings

The average I calculate is not within -10 to 10, it is on the order of -1000 to 1000 On Thu, Jan 20, 2011 at 3:11 PM, Dallas Warren wrote: > You have a variable that is fluctuating over a range of 800+ units (three > orders of magnitude) and want the average to be 1.0? > > > > It is not a problem

Re: [gmx-users] Inaccurate pressure readings

from -1000 to 1000, depending on the system. The simulation box is 8x8x8 nm (roughly) and contains about 12,000 atoms On Thu, Jan 20, 2011 at 3:09 PM, Justin A. Lemkul wrote: > > > Denny Frost wrote: > >> I am running a variety of NPT simulations with polar, non-polar, and ionic >> compounds.

Re: [gmx-users] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3

Gee. My mistake then. I did not realize the difference between -COO and Zwitterion_COO-. However, when I use the zwitterion termini on both ends of the other chain, the total charge is 4.010, which is also *slightly*´ disturbing. I have seen numbers like 2.99, which are still better. Is 4.010

Re: [gmx-users] Inaccurate pressure readings

Denny Frost wrote: from -1000 to 1000, depending on the system. The simulation box is 8x8x8 nm (roughly) and contains about 12,000 atoms Are the systems even stable? Is there a trend in the pressure, or is it stable at those values? It seems that the systems are either exploding or impl

Re: [gmx-users] non-integer charge in a protein setup using pdb2gmx AND slow simulations in vacuum v. 4.5.3

maria goranovic wrote: Gee. My mistake then. I did not realize the difference between -COO and Zwitterion_COO-. However, when I use the zwitterion termini on both ends of the other chain, the total charge is 4.010, which is also *slightly*´ disturbing. I have seen numbers like 2.99, whi

Re: [gmx-users] Inaccurate pressure readings

Sorry about forgetting the simulation time. They run for about 12 ns, at which point I stop them. They appear stable - the box vectors don't change a lot (which is surprising since the pressure sure does). Below is a complete mdp file. title = Run1 cpp = /lib/cp

RE: [gmx-users] Inaccurate pressure readings

Then something you have said isn't right. In first email you said that the pressure varies between -400 and +400 bar. Now you say that the average can vary from -1000 to +1000 bar. If the instantaneous pressure is varying from -1000 to +1000 bar, then that is not a real issue. However, if the av

Re: [gmx-users] Inaccurate pressure readings

This seems odd. If a value fluctuates between -400 and +400, how can the average be outside the range? Warren Gallin On 2011-01-20, at 3:24 PM, Denny Frost wrote: > from -1000 to 1000, depending on the system. The simulation box is 8x8x8 nm > (roughly) and contains about 12,000 atoms > > On

Re: [gmx-users] Inaccurate pressure readings

Denny Frost wrote: Sorry about forgetting the simulation time. They run for about 12 ns, at which point I stop them. They appear stable - the box vectors don't change a lot (which is surprising since the pressure sure does). Below is a complete mdp file. If the box vectors aren't chang

Re: [gmx-users] Inaccurate pressure readings

Sorry, I'm referring to a lot of runs here - some fluctuate more than others and some have greater average values than others. The average value is never greater than the maximum fluctuation in each run, so that is not a problem. The average given by g_energy, however, is not close to 1.0 bar in

Re: [gmx-users] Inaccurate pressure readings

On 21/01/2011 10:12 AM, Denny Frost wrote: Sorry, I'm referring to a lot of runs here - some fluctuate more than others and some have greater average values than others. The average value is never greater than the maximum fluctuation in each run, so that is not a problem. The average given by

[gmx-users] Problem with using topolbuild1_3.tgz

Hi, I am trying to generate topology files for a set of lipids with the help of topolbuild1_3.tgz package found at the other software page of GROMACS website. I downloaded and installed all files and tried running the program with a MOL2 file with charges in it. However, it shows an error message

[gmx-users] Running a crashed run

Hi, I am running a crashed run (orgininally for a 3ns simulation) but at the time of rerunning I forgot to assign -v tag in the command and now I an not able to know at which step the simulation is going on .. For that I check the state.cpt file , actually there are two .cpt files one with state.c

Re: [gmx-users] Running a crashed run

bharat gupta wrote: Hi, I am running a crashed run (orgininally for a 3ns simulation) but at the time of rerunning I forgot to assign -v tag in the command and now I an not able to know at which step the simulation is going on .. For that I check the state.cpt file , actually there are two

Re: [gmx-users] How to install a new Forcefield in Gromacs 4.5.3

2011/1/20 Justin A. Lemkul > > > Qin Qiao wrote: > >> >> >> 2011/1/20 Justin A. Lemkul mailto:jalem...@vt.edu>> >> >> >> >>Qin Qiao wrote: >> >> >> >>2011/1/20 Justin A. Lemkul > > >>>> >> >> >> >

Re: [gmx-users] How to install a new Forcefield in Gromacs 4.5.3

Qin Qiao wrote: 2011/1/20 Justin A. Lemkul mailto:jalem...@vt.edu>> Qin Qiao wrote: 2011/1/20 Justin A. Lemkul mailto:jalem...@vt.edu> >> Qin Qiao wrote: 2011/1/20 Justin A. Lemkul mailto

Re: [gmx-users] How to install a new Forcefield in Gromacs 4.5.3

In the first instance of creating a new forcefield, do so in your working directory - create myforcefield.ff directory and fill it with your fields. pdb2gmx 4.5.x will find this and let you use it according to the name in forcefield.doc (IIRC). Once you have it working properly, then consider i

Re: [gmx-users] How to install a new Forcefield in Gromacs 4.5.3

2011/1/21 Justin A. Lemkul > > > Qin Qiao wrote: > >> >> >> 2011/1/20 Justin A. Lemkul mailto:jalem...@vt.edu>> >> >> >> >>Qin Qiao wrote: >> >> >> >>2011/1/20 Justin A. Lemkul > >>> >> >> >> >>

Re: [gmx-users] How to install a new Forcefield in Gromacs 4.5.3

Qin Qiao wrote: 2011/1/21 Justin A. Lemkul mailto:jalem...@vt.edu>> Qin Qiao wrote: 2011/1/20 Justin A. Lemkul mailto:jalem...@vt.edu> >> Qin Qiao wrote: 2011/1/20 Justin A. Lemkul mailto

Re: [gmx-users] How to install a new Forcefield in Gromacs 4.5.3

2011/1/21 Justin A. Lemkul > > > Qin Qiao wrote: > >> >> >> 2011/1/21 Justin A. Lemkul mailto:jalem...@vt.edu>> >> >> >> >> >>Qin Qiao wrote: >> >> >> >>2011/1/20 Justin A. Lemkul > >>> >> >> >> >

Re: [gmx-users] How to install a new Forcefield in Gromacs 4.5.3

Qin Qiao wrote: 2011/1/21 Justin A. Lemkul mailto:jalem...@vt.edu>> Qin Qiao wrote: 2011/1/21 Justin A. Lemkul mailto:jalem...@vt.edu> >> Qin Qiao wrote: 2011/1/20 Justin A. Lemkul mailt

[gmx-users] Regarding g_analyze

Hi, After completing my simulation , I have generated the potential.xvg file and also I generated the average of the potential for the whole simulation using g_analyze. But when I open the file average.avg I shows me the same graph as that of potential.xvg but with red color.. What I want is a re

Re: [gmx-users] Regarding g_analyze

bharat gupta wrote: Hi, After completing my simulation , I have generated the potential.xvg file and also I generated the average of the potential for the whole simulation using g_analyze. But when I open the file average.avg I shows me the same graph as that of potential.xvg but with red

[gmx-users] Visualizing the simulation in VMD

I loaded the .gro file generated after pdb2gmx command in vmd and then I loaded the .trr file into that molecule but it shows frame 1 vol 0 in VMD and when I click the play button on the toolbar the frames doesn't move ... can anybody tell me how to play the simula tion in VMD ?? or where am i goin

Re: [gmx-users] Regarding g_analyze

bharat gupta wrote: I generated this graph using xyplot since I was not able to install xmgrace on windows platform .. also I want to one more thing ... that I calculated the rmsd and rmsd_xtal graph .. I found them to be same and the fluctuations in graph is same for 0 to 1.5 nm and then l

Re: [gmx-users] Visualizing the simulation in VMD

bharat gupta wrote: I loaded the .gro file generated after pdb2gmx command in vmd and then I loaded the .trr file into that molecule but it shows frame 1 vol 0 in VMD and when I click the play button on the toolbar the frames doesn't move ... can anybody tell me how to play the simula tion in

RE: [gmx-users] Visualizing the simulation in VMD

This is more of a question you should be directing to the VMD emailing list. How many frames does your .trr file contain? Use gmxcheck to see what the .trr file contains. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Mona

Re: [gmx-users] Regarding g_analyze

It means that rmsd plot is stable .. I am trying to run the trajectory in windows using VMD and for that i followed what was said in past thread of gmx discussion list but I am not able to run the trajectory and for that I have posted another question regarding that jus 5 mins back.. Also if u ca

Re: [gmx-users] Regarding g_analyze

bharat gupta wrote: It means that rmsd plot is stable .. I am trying to run the trajectory in windows using VMD and for that i followed what was said in past thread of gmx discussion list but I am not able to run the trajectory and for that I have posted another question regarding that jus 5

Re: [gmx-users] Visualizing the simulation in VMD

On Thu, Jan 20, 2011 at 7:44 PM, Justin A. Lemkul wrote: > > > bharat gupta wrote: > >> I loaded the .gro file generated after pdb2gmx command in vmd and then I >> loaded the .trr file into that molecule but it shows frame 1 vol 0 in VMD >> and when I click the play button on the toolbar the fram

Re: [gmx-users] Visualizing the simulation in VMD

bharat gupta wrote: After running the simulation I checked the trajectory in using ngmx in some other system .. and it was working .. since I need to do some more analysis during trajectory run on my protein I thought of running into VMD and I used the file .trr after completng the simulat

[gmx-users] Re: avoiding bad contact in continutation run (Mark Abraham)

1. Re: avoiding bad contact in continutation run (MarkAbraham) Adwait Mevada wrote: On 01/20/11, Adwait Mevada wrote: Dear gmx-users, I am simulating a dppc + chol system, the force field is martini with gromacs 3.3.3 the system was initially run for 150 ns, but i had to later ex

Re: [gmx-users] Re: avoiding bad contact in continutation run (Mark Abraham)

> one final query, i need the new tpr to have a different output frequency than > the older one, is there a way to achieve that. > Thanks, > -Adwait > > You have to use the grompp version of restarts for that. See the URL I gave earlier. Mark -- gmx-users mailing listgmx-users@gromacs.

[gmx-users] charge group radii larger that rlist-rvdw

Dear gromacs users, I am using gromacs 4.5.3, OPLSAA force field, and the cut off parameters are as shown below: - ;NEIGHBOURSEARCHING PARAMETERS nstlist = 10 10 ; FREQU

[gmx-users] RE: RMSD calculation of a specific region

I want to calculate the rmsd of amino acid 65 to 67 of two simulated proteins with loop replacement in another one to find out how the position of these 3 amino acids change due to the replacement of a loop region in same protein ... How can I achieve it with gromacs... -- Bharat Ph.D. Candidat

[gmx-users] decorrelation function

Hello! I wanted to ask where I can analyze decorrelation functions of, for instance, bonds and torsions? I have the tool g_analyze with option -ac. Here I get negative values, but I thought that the function is in a range between 0 and 1. I would like to have the P2 decorrelation function, so I