[gmx-users] Is it flexible water or all the bond, angle fixed? what is the potential energy in Gromacs 4.5 using OPLSAA

Hi gromacs experts, I used gromacs 4.5.3. my system has only spce water, no other types. In .mdp file, I used the following parameters; define = constraints = none constraint-algorithm = Lincs Can u tell me Is it flexible water or all the bond, angle fixed using the above setting?

[gmx-users] Re:gmx-users Digest, Vol 84, Issue 207

Hi Justin, When i define define = FLEXIBLE constraints = none constraint-algorithm = Lincs I saw my .log file. Input Parameters: integrator = md nsteps = 1 init_step= 0 ns_type = Grid nstlist = 5

[gmx-users] can Gromacs 4.5 use VDW long range correction? IN the mannual, In this version, GROMACS always uses a cut-off radius for the Lennard-Jones interactions

UN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit = 0 dt = 0.001 nsteps = 40 ; For exact run continuation or redoing part of a run init_step = 0 ; mode for center of mass motion removal comm-mode = Linear ; number of steps for center of mass motion removal n

[gmx-users] Fw:Re:gmx-users Digest, Vol 97, Issue 218

ecific >than "Re: Contents of gmx-users digest..." > > >Today's Topics: > > 1. can Gromacs 4.5 use VDW long range correction? IN the > mannual, In this version, GROMACS always uses a cut-off radius > for the Lennard-Jones interactions (MD) > 2. Re:

[gmx-users] surface tension, Long range LJ correction, TIP4P/2005

: FALSE I spend two weeks on this ,but still failed to know the reason, because only myself do MD in my department. Can anyone help?? title= Yo cpp = /usr/bin/cpp include = define = integrator = md tinit

[gmx-users] tip5p tip, not good, energy can only get -39, not -45

HI All, I run the tip5p water model, i found the computed properties are not good, e.g. energy. Can anyone know the problem? i need to get the surface potential, it can get -1 V regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Plea

[gmx-users] 2nd Virial coefficient and Hydrophobic moment Calculation

Hi GMX user, Is there anyway I can calculate 2nd virial coefficient and hydrophobic moment using gromacs? I guess 2nd virial coefficient calculated somewhere in the gromacs. Thanking you, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] P

RE: [gmx-users] 2nd Virial coefficient and Hydrophobicmoment Calculation

: [EMAIL PROTECTED] on behalf of David van der Spoel Sent: Fri 22/06/2007 8:40 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] 2nd Virial coefficient and Hydrophobicmoment Calculation Naser, Md Abu wrote: > Hi GMX user, > > Is there anyway I can calculate 2nd virial co

[gmx-users] rotational fit in XY plane only

> > I implemented an xy only fitting option for trjconv in the development > > branch. > > > > Berk. In reference to the above replay of Berk, I was trying to get into CVS to get a copy of it. When I click on the "instructions on how to access our CVS repository", it says not authorised to acce

[gmx-users] g_wham

Hi, Is there any way I can get corrected version of g_wham? I know form the discussion archive that David Bostick has a copy of the corrected g_wham. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265

[gmx-users] g_sorient segmenation fault

Hi All, I have been getting segmenation fault with current(3.3.1) version of g_sorient. Dose anybody know why? With best regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 ___

RE: [gmx-users] g_wham

hi Lanyuan, Thanks for your replay. I have tried the current(3.3.1) and 3.3 version g_wham. They both dont work. What do you mean by original? With best regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 F

[gmx-users] atom index number

Hi Gmx user, I have wondering whether it is possible to extract index numbers for atoms from a particular region in the box such as, if a box divided into 10 slices along z and one wants to get all the atom's index number of protein in 1st slice or 3rd, etc. With regards, Abu Naser School

[gmx-users] g_energy -fee -inf problem

Hi All User, I am getting free energy difference -inf. 1st I run a protein in water molecule and then I made a different topology file with deleting 4 disulfide bonds and accordingly the angles and diherdal angles. Then, I run -rerun for the both and and g_energy -fee, which giving me free energy

RE: [gmx-users] atom index number

with trjconv, then process it with aforementioned tools. /Erik 21 sep 2007 kl. 17.33 skrev Naser, Md Abu: > Hi Gmx user, > > I have wondering whether it is possible to extract index numbers > for atoms from a particular > region in the box such as, if a box divided into 10 slices

RE: [gmx-users] g_energy -fee -inf problem

PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of Mark Abraham Sent: Sat 22/09/2007 6:05 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_energy -fee -inf problem Naser, Md Abu wrote: > Hi

RE: [gmx-users] g_energy -fee -inf problem

TED] on behalf of Mark Abraham Sent: Mon 24/09/2007 9:02 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_energy -fee -inf problem Naser, Md Abu wrote: > Hi Mark, > > Thank you very much for your replay.I was just trying to > calculate free energy difference between

RE: [gmx-users] g_energy -fee -inf problem

PROTECTED] on behalf of Mark Abraham Sent: Mon 24/09/2007 9:22 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_energy -fee -inf problem Naser, Md Abu wrote: > Hi Mark, > > The reacton shuld occur as: R-S-S-R + 2H+ -> 2R-SH. So at the very least, your "after&qu

[gmx-users] g_dist

Hi all user, I have just calculated a distance between backbone and side chain of the same protein. I get negative distance along x and y direction. What dose negative distance mean? Thanks in advance. Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [E

RE: [gmx-users] g_dist

] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of David van der Spoel Sent: Tue 25/09/2007 9:42 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_dist Naser, Md Abu wrote: > > > Hi all user, > &

RE: [gmx-users] g_dist

Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of Xavier Periole Sent: Tue 25/09/2007 10:13 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_dist On Tue, 25 Sep 2007 10:03:30 +0100 "Naser, Md Abu" <[EMAIL PROTECTED]

RE: [gmx-users] g_dist

MACS users > Subject: Re: [gmx-users] g_dist > > On Tue, 25 Sep 2007 10:03:30 +0100 > "Naser, Md Abu" <[EMAIL PROTECTED]> wrote: >> Hi David, >> >> Yes, it should be a vector as it is a difference between the center of mass >>of two groups

[gmx-users] make_ndx

Hi All User, Is there anyway I can single out side chain of alpha carbon atom using make_ndx? Thanks in advance. Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009

RE: [gmx-users] make_ndx

+44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf of Xavier Periole Sent: Wed 26/09/2007 8:42 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] make_ndx On Wed, 26 Sep 2007 20:08:06 +0100 "Naser, Md Abu" <[EMAIL PROTECTED

RE: [gmx-users] make_ndx

: Discussion list for GROMACS users Subject: Re: [gmx-users] make_ndx Naser, Md Abu wrote: > Hi XAvier, > > "Single out" I mean pick up only the side chain bonded with alpha > carbon atom and > put them in a group using make_ndx. > all side chains are. and sidechain

RE: [gmx-users] make_ndx

PROTECTED] on behalf of David van der Spoel Sent: Thu 27/09/2007 7:29 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] make_ndx Naser, Md Abu wrote: > Thanks david! > oops I misread. Sidechains do not contain C-alpha (which you can easily check in the index file). So

[gmx-users] qasi-harmonic entropy calculation

Hi all user, I have calculated entroy over time from eigenvalue(g_covar) and the result shows that the entropy decreasing towards zeo. The results is ok as far as it decreases. But I do not understand why it is approaching to zero towards the end of the simulation. Can anyone explain why? I wo

RE: [gmx-users] qasi-harmonic entropy calculation

the entropy? Are you calculating it in dt time frames or are your results cumulative? Why do you expect the entropy to decrease? Regards, Pedro. 2007/10/18, Naser, Md Abu <[EMAIL PROTECTED]>: > > Hi all user, > > I have calculated entroy over time from eigenvalue(g_covar) and

RE: [gmx-users] qasi-harmonic entropy calculation

Hi David, Thanks for your information and I will have a look CVS head version. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAI

RE: [gmx-users] qasi-harmonic entropy calculation

, Naser, Md Abu <[EMAIL PROTECTED]>: > > Hi Pedro, > > Thank you for your attention to my email. Yes, I am using Schlitter > equation and the > rusult is cumulative. The entropy is meant to be decreased as the protein > is stick > on to a surface. > > I have use

RE: [gmx-users] regarding comm_mode

Because in periodic or assymmetric system, the angular momentum is not conserved. You can find the explaination in computer simulation of liquids - Allen and Tldesley.   Best wishes,   Abu Naser   From: [EMAIL PROTECTED]Sent: Mon 14/08/2006 11:58 AMTo: gmx-users@gromacs.orgSubject: [gmx-use

RE: [gmx-users] range checking error

-Original Message- From: [EMAIL PROTECTED] on behalf of Giacomo Bastianelli Sent: Tue 05/12/2006 10:16 AM To: Discussion list for GROMACS users Subject: [gmx-users] range checking error Dear Users, I am running MD of an homology model and even with a long energy minimization step a

RE: [gmx-users] problem regarding do_dssp

Try running with -v option. It might give you clue where is the problem. Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009 -Original Message- From: [EMAIL PROTECTED] on behalf

RE: [gmx-users] problem still lies regarding dssp

Hi Sangeeta, Let me ask you few questions in order to solve the problem. Are you sure your do_dssp prog were running or it was hanged? To make sure please try using verbose output using -v option. Is your computer shared among too many people? What is the file permission status of dssp? To f

RE: [gmx-users] problem still lies regarding dssp

er to get taht particular coloured map what procedure should I adopt?? regards SANGEETA "Naser, Md Abu " <[EMAIL PROTECTED]> wrote: Hi Sangeeta, Let me ask you few questions in order to solve the problem. Are you sure your do_dssp prog were running or it was hang

[gmx-users] Decabe density

Title: Decabe density Hi All User, I have made a decane box of roughly about 730gm/liter  but when I allow vaccuume or put water for making an interface, it changes its density to roughly about 800gm/ liter or more  on 2ns run. Is there anyone knows why this is happening? Abu Naser Schoo

[gmx-users] distance measurement

Title: distance measurement Hi All, Is there anyway I can measure distance between protein and edge of a box in z direction? Regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009

RE: [gmx-users] distance measurement

take half of that. You could ofcourse take the maximal z-coordinate and subtract it from the third number of the last line of the .gro file (which gives the z component of the third box vector). Cheers, Tsjerk On 3/30/06, Naser, Md Abu <[EMAIL PROTECTED]> wrote: > > Hi All, >

[gmx-users] comm-mode = Angular

Hi All,   Dose anyone know any literature regarding comm-mode = Angular option? With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email: [EMAIL PROTECTED] Phone: +44(0)1314518265 Fax : +44(0) 131 451 3009    

RE: [gmx-users] comm-mode = Angular

+44(0)1314518265 Fax : +44(0) 131 451 3009   From: David van der SpoelSent: Tue 25/04/2006 7:32 PMTo: Discussion list for GROMACS usersSubject: Re: [gmx-users] comm-mode = Angular Naser, Md Abu wrote: > Hi All, > > Dose anyone know any literature regarding comm-mode = Angular o

RE: [gmx-users] comm-mode = Angular

x27;t have the time either :S However, you can download my versions at http://md.chem.rug.nl/~tsjerk/GMX/Cheers,Tsjerk On 4/26/06, Naser, Md Abu <[EMAIL PROTECTED]> wrote: Hi Tsjerk, I have been wondering whether Andrea Amadei  and coworkers' method ( J. Chem. Phys. 112(1) pp. 9-23)