[gmx-users] pulling of ligand

Dear GMX user I am working on enzyme ligand complex and want to calculate pmf of the complex. I have successfully energy minimized and equilibrated the system. But when I pull the ligand from the complex using the md_pull.mdp file then instead of ligand the protein is come out of the system. I ha

[gmx-users] Centre of mass removal in CGMD

Hi ALL, I am trying to simulate a protein inserted in a lipid bilayer with water and ions, the entire system built using CG (coarse grain). I am using the Martini force field to the CGMD simulation. My question is that should I use the "centre of mass removal" component in my .mdp file (which we d

RE: [gmx-users] Units of k1 in the pulling code

> Date: Thu, 12 Aug 2010 17:33:09 -0400 > From: chris.ne...@utoronto.ca > To: gmx-users@gromacs.org > Subject: [gmx-users] Units of k1 in the pulling code > > Dear Xueming: > > the word "mol" is short form for "mole" > > http://en.wikipedia.org/wiki/Mole_%28unit%29 > > In the pull code conte

Re: [gmx-users] umbrella histograms

Dear Chris Thanks but I am not using periodic boundary conditions as I want to simulate the two molecules in a vacuum. Gavin chris.ne...@utoronto.ca wrote: > Dear Gavin: > > plot the position vs. time. Probably you will see it sample around one > value, then discover a new state, and make a sha

Re: [gmx-users] Centre of mass removal in CGMD

On Aug 13, 2010, at 10:00 AM, Anirban Ghosh wrote: Hi ALL, I am trying to simulate a protein inserted in a lipid bilayer with water and ions, the entire system built using CG (coarse grain). I am using the Martini force field to the CGMD simulation. My question is that should I use the "

Re: [gmx-users] Centre of mass removal in CGMD

Thanks a lot XAvier. And if one wants to study the self assembly of a GPCR using CGMD (like you did for rhodopsin), should he/she use the same parameters for COM motion removal? Regards, Anirban On Fri, Aug 13, 2010 at 3:18 PM, XAvier Periole wrote: > > On Aug 13, 2010, at 10:00 AM, Anirban G

Re: [gmx-users] Centre of mass removal in CGMD

On Aug 13, 2010, at 12:37 PM, Anirban Ghosh wrote: Thanks a lot XAvier. And if one wants to study the self assembly of a GPCR using CGMD (like you did for rhodopsin), should he/she use the same parameters for COM motion removal? I guess so :)) Regards, Anirban On Fri, Aug 13, 2010 at 3

Re: [gmx-users] pulling of ligand

abdul wadood wrote: Dear GMX user I am working on enzyme ligand complex and want to calculate pmf of the complex. I have successfully energy minimized and equilibrated the system. But when I pull the ligand from the complex using the md_pull.mdp file then instead of ligand the protein is com

[gmx-users] Re: "Re: Segmantation fault at g_traj"

Jorge Alberto Jover Galtier wrote: Hi, Justin. Thank you for answering so quickly. We write you directly because we receive the daily digest from Gromacs and we are not sure how to answer to the thread. We have tried what you suggested, using 10,000 steps and Reply to the message, strip o

[gmx-users] the mdrun choked or maybe braked.

Hi, The problem just like this, in md.log There are: 130889 Atoms splitting topology... Walking down the molecule graph to make constraint-blocks There are 43925 charge gro

Re: [gmx-users] the mdrun choked or maybe braked.

#ZHAO LINA# wrote: Hi, The problem just like this, in md.log There are: 130889 Atoms splitting topology... Walking down the molecule graph to make constraint-blocks The

RE: [gmx-users] the mdrun choked or maybe braked.

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, August 13, 2010 7:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] the mdrun choked or maybe braked. #ZHA

Re: [gmx-users] the mdrun choked or maybe braked.

#ZHAO LINA# wrote: From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, August 13, 2010 7:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] the mdrun choked

[gmx-users] Question about g_hbond output

Hi evergyone, I analysed the number of hydrogenation bond with Gromacs 4.0.4 by running g_hbond -s md.tpr -f md.xtc -num numhbond.xvg There are 3 columns in the output files. The first column = frame The second column = H bonds The third column = pairs within 0.35nm The third colu

Re: [gmx-users] Question about g_hbond output

Jinyao Wang wrote: Hi evergyone, I analysed the number of hydrogenation bond with Gromacs 4.0.4 by running g_hbond -s md.tpr -f md.xtc -num numhbond.xvg There are 3 columns in the output files. The first column = frame The second column = H bonds The third column = pairs within 0.

[gmx-users] ener.edr

Hello, Does gromacs write the current values (at some requested step) to ENER.EDR or the averaged ones (at the requested interval)? -- Dr. Vitaly Chaban Associate Researcher Department of Chemistry University of Roshester, Rochester, NY 14642 -- gmx-users mailing listgmx-users@gromacs.org h

[gmx-users] editconf

Hello, I'd like to ask a question about the conversion of the results of minimization to pdb format. Here is what I do: Apply pdb2gmx to the pdb file to convert it to .gro and .top (pdb2gmx -f -p -o)Run editconf to define the box (editconf -d 1)run gromp and mdrun for the minimizationRun e

[gmx-users] ener.edr

The .edr file contains the instantaneous energies at every nstenergy steps. -- original message -- Hello, Does gromacs write the current values (at some requested step) to ENER.EDR or the averaged ones (at the requested interval)? -- gmx-users mailing listgmx-users@gromacs.org http://list

Re: [gmx-users] editconf

abdullah ahmed wrote: Hello, I'd like to ask a question about the conversion of the results of minimization to pdb format. Here is what I do: 1. Apply pdb2gmx to the pdb file to convert it to .gro and .top (pdb2gmx -f -p -o) 2. Run editconf to define the box (editconf -d 1)

Re: [gmx-users] editconf

-- Chandan kumar Choudhury NCL, Pune INDIA On Fri, Aug 13, 2010 at 8:08 AM, Justin A. Lemkul wrote: > > > abdullah ahmed wrote: > >> Hello, >> >> I'd like to ask a question about the conversion of the results of >> minimization to pdb format. Here is what I do: >> >> 1. Apply pdb2gmx to the p

RE: [gmx-users] ener.edr

To be more precise, it writes both the current values and the sum over the steps to let g_energy print exact averages. Berk > Date: Fri, 13 Aug 2010 11:08:24 -0400 > From: chris.ne...@utoronto.ca > To: gmx-users@gromacs.org > Subject: [gmx-users] ener.edr > > The .edr file contains the instanta

Re: [gmx-users] umbrella histograms

Dear Chris In relation to the correspondence below, I should've mentioned that the peaks are symmetrical about the equilibrium distance as supposed to the there being one main peak at the equilibrium distance. Also should there be much of difference if you set pull_init to equal the distance betwe

[gmx-users] RE: ener.edr

Berk, if I need the average values between 0...N, N...2N, etc - what is the convenient way to get them automatically (in energy.xvg)? Thank you, Vitaly >To be more precise, it writes both the current values and >the sum over the >steps >to let g_energy print exact averages. -- gmx-users mailin

[gmx-users] umbrella histograms

As I said before, please plot the position vs. time. It would be best if you can make a graph of this and post it to some web tool. I use photobucket, but there are many others. I realize that you think you are starting at equilibrium, but there are always things that can have unexpected co

RE: [gmx-users] RE: ener.edr

In version 4.0 g_energy -aver prints the sum up till time t. You then have to subtract the value at the previous step and divide by the number of steps between frames. You can also download 4.5-beta, there g_energy -aver will directly print the averages over the last -nstenergy steps, also of edr

Re: [gmx-users] umbrella histograms

Thanks Chris I have equilibrated the system at 600 K in a previous run therefore would it not be equilibrated, and also would the velocities from the final configuration of the equilibration not be sufficient as equilibrium velocities going into the main simulation Gavin chris.ne...@utoronto.ca

[gmx-users] umbrella histograms

Gavin, I wish you the best of luck. Perhaps somebody else on the list can help you. -- original message -- Thanks Chris I have equilibrated the system at 600 K in a previous run therefore would it not be equilibrated, and also would the velocities from the final configuration of the equilibra

Re: [gmx-users] umbrella histograms

Chris Cheers and thanks for the suggestions. P.S. I hope you don't think that the previous msg was in anyway rude. It was actually a genuine question :) Cheers GAvin chris.ne...@utoronto.ca wrote: > Gavin, I wish you the best of luck. Perhaps somebody else on the list > can help you. > > -- or

[gmx-users] ener.edr & -[no]aver

Also, is anybody aware of what the following option of g_energy performs: -[no]averbool yes Print also the X1,t and sigma1,t, only if only 1 energy is requested If I compare the results of 'g_energy' and 'g_energy -aver', the numbers are the same. Does it mean that g_energy print the av

[gmx-users] tpi segmentation fault

Hi all. I am trying to perform a tpi (test particle insertion) calculation on a trajectory generated with mpi_mdrun (gromacs 4.0.7, run in a Beowulf cluster of Intel(R) Core(TM)2 Quad CPUQ6600 @ 2.40GHz). I am using tpi integrator in the mdp file and the following command: $ grompp -f

Re: [gmx-users] Problem with removing COM translation

On 12/08/10 15:25, Alexandre Suman de Araujo wrote: I'm simulating a system composed by a protein centered in a sphere of water in vacuum. The water molecules are kept within a virtual sphere with position restrains between oxygen atom and a dummy atom fixed at the center of the sphere. The prot

Re: [gmx-users] Problem with removing COM translation

Em 13-08-2010 14:24, ms escreveu: On 12/08/10 15:25, Alexandre Suman de Araujo wrote: I'm simulating a system composed by a protein centered in a sphere of water in vacuum. The water molecules are kept within a virtual sphere with position restrains between oxygen atom and a dummy atom fixed a

[gmx-users] PCA

I have done PCA using first g_covar and got eigval.xvg and eigenvec.trr files. The eigenvectors were analyzed by g_anaeig program and got eigcomp.xvg, eigrmsf.xvg, proj.xvg, and 2dproj.xvg files. Then I want to know 1. Which file among these shows relative positional fluctuation with eigenvector in

Re: [gmx-users] Problem with removing COM translation

On 13/08/10 18:30, Alexandre Suman de Araujo wrote: I am just curious but... why are you doing actually all of this instead of using a normal periodic solvent box? The idea is to have less water molecules and, consequently, faster simulations. I thought about that, but I guessed you can use

Re: [gmx-users] GPU CUDA version does not support improper dihedrals?

Hi, We discussed this a bit off-list, and just figured it would be good to include the conclusions here too so people find it if they search the archives. First, we definitely support all improper torsions of periodic form, such as those in amber, charmm, and opls in OpenMM too, while Gromos us

[gmx-users] Check V for NVT‏

Hi Gmx users, I am using 4.0.X version of Gromacs and doing a NVT simulation. Now I wanna check if the Volume is constant after the simulation. I tried g_energy but did not find "Volume" in the pool of the options. Can anyone help me? Thanks, Juju -- gmx-users mailing listgmx-u

Re: [gmx-users] Check V for NVT‏

Rama G wrote: Hi Gmx users, I am using 4.0.X version of Gromacs and doing a NVT simulation. Now I wanna check if the Volume is constant after the simulation. I tried g_energy but did not find "Volume" in the pool of the options. Can anyone help me? Box-X, -Y, and -Z are in the .edr file.

Re: [gmx-users] Check V for NVT‏

On Fri, 13 Aug 2010 18:23:40 -0400 "Justin A. Lemkul" wrote: > Rama G wrote: > > Hi Gmx users, > > > > I am using 4.0.X version of Gromacs and doing a NVT simulation. Now > > I wanna check if the Volume is constant after the simulation. > > I tried g_energy but did not find "Volume" in the pool o

Re: [gmx-users] Check V for NVT‏

Jussi Lehtola wrote: On Fri, 13 Aug 2010 18:23:40 -0400 "Justin A. Lemkul" wrote: Rama G wrote: Hi Gmx users, I am using 4.0.X version of Gromacs and doing a NVT simulation. Now I wanna check if the Volume is constant after the simulation. I tried g_energy but did not find "Volume" in the p

Re: [gmx-users] Check V for NVT‏

Thanks Justin, but I did not find them, what I found are Vir-XY, YZ, XX, Are these the same as Box-X, Y, Z, or perhaps can be converted to? Btw, I am using 4.0.7 version. One more Q', I saw your great gromacs tutor...@vt, but I am kinda confused you used both NPT and NVT in position restrain

Re: [gmx-users] Check V for NVT‏

Thanks guys, Sorry, I did not find "Density" in version 4.0.7. nor Box-X, Y, Z. Any other way out? Best, Juju From: Jussi Lehtola To: gmx-users@gromacs.org Sent: Fri, August 13, 2010 3:29:56 PM Subject: Re: [gmx-users] Check V for NVT‏ On Fri, 13 Aug 2010

Re: [gmx-users] Check V for NVT‏

When you run an NVT simulation the box coordinates are not written out in the edr file. You can try to extract the box information from your trajectory files. On Fri, Aug 13, 2010 at 6:42 PM, Rama G wrote: > > Thanks guys, > > Sorry, I did not find "Density" in version 4.0.7. nor Box-X, Y, Z. >

Re: [gmx-users] Check V for NVT‏

Rama G wrote: Thanks Justin, but I did not find them, what I found are Vir-XY, YZ, XX, Are these the same as Box-X, Y, Z, or perhaps can be converted to? Btw, I am using 4.0.7 version. See the latest post in the thread. The Vir-* terms refer to virial, which is unrelated. One more Q

Re: [gmx-users] Check V for NVT‏

Rama G wrote: Thanks guys, Sorry, I did not find "Density" in version 4.0.7. nor Box-X, Y, Z. Any other way out? The very absence of these terms indicates that your volume was constant. What purpose do you have for checking it? Do you think something went wrong? If a simple NVT didn't

[gmx-users] umbrella histograms

Your language was not rude, but I did get frustrated after twice asking you to perform an analysis and twice being ignored. My advice still stands: plot the deviation vs. time and report back to the list. Chris. -- original message -- Cheers and thanks for the suggestions. P.S. I hope you

Re: [gmx-users] editconf

- Original Message - From: abdullah ahmed Date: Saturday, August 14, 2010 1:05 Subject: [gmx-users] editconf To: gmx --- | > Hello, > > I'd like to ask a question about the conversion of the results of > minimization to pdb for

[gmx-users] g_gyrate -p => Calculate the radii of gyration about the principal axes

Hi To Calculate the radii of gyration about the principal axes I use the command g_gyrate -p For lysozyme , I got => 0.922754 1.22249 1.25603 but in some paper, the authors got => 0.660 0.833 0.991 It is a quite difference. what is the definition of the radii of gyration about the

[gmx-users] Parallel mdrun not working on gentoo linux

Hi All, I am trying to build gromacs-4.0.7 on my gentoo box. My non-parallel version of mdrun is working without any issues but when I try to run the parallel version of mdrun, it kind of hangs (even no help info). Some details- 1) $uname -a Linux bingo 2.6.34-gentoo-r1 #7 SMP Fri Aug 13 10:18:23