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

2007-10-19 Thread Naser, Md Abu
, 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] qasi-harmonic entropy calculation

2007-10-18 Thread Naser, Md Abu
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

2007-10-18 Thread Naser, Md Abu
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

[gmx-users] qasi-harmonic entropy calculation

2007-10-18 Thread Naser, Md Abu
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] make_ndx

2007-09-26 Thread Naser, Md Abu
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

RE: [gmx-users] make_ndx

2007-09-26 Thread Naser, Md Abu
: 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

2007-09-26 Thread Naser, Md Abu
+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

[gmx-users] make_ndx

2007-09-26 Thread Naser, Md Abu
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] g_dist

2007-09-25 Thread Naser, Md Abu
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

RE: [gmx-users] g_dist

2007-09-25 Thread Naser, Md Abu
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

2007-09-25 Thread Naser, Md Abu
] 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, > &

[gmx-users] g_dist

2007-09-25 Thread Naser, Md Abu
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_energy -fee -inf problem

2007-09-24 Thread Naser, Md Abu
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

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

2007-09-24 Thread Naser, Md Abu
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

2007-09-24 Thread Naser, Md Abu
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] atom index number

2007-09-24 Thread Naser, Md Abu
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

[gmx-users] g_energy -fee -inf problem

2007-09-22 Thread Naser, Md Abu
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

[gmx-users] atom index number

2007-09-21 Thread 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 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

RE: [gmx-users] g_wham

2007-09-14 Thread Naser, Md Abu
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] g_sorient segmenation fault

2007-09-14 Thread Naser, Md Abu
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 ___

[gmx-users] g_wham

2007-09-14 Thread Naser, Md Abu
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] rotational fit in XY plane only

2007-06-26 Thread Naser, Md Abu
> > 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

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

2007-06-22 Thread Naser, Md Abu
: [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] 2nd Virial coefficient and Hydrophobic moment Calculation

2007-06-20 Thread Naser, Md Abu
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] problem still lies regarding dssp

2007-02-12 Thread Naser, Md Abu
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

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

2007-02-09 Thread Naser, Md Abu
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 regarding do_dssp

2007-02-05 Thread Naser, Md Abu
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] range checking error

2006-12-05 Thread Naser, Md Abu
Hi Giacomo, That is due to the bad starting structure. You might want to try with small time step and with no constrain. 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] regarding comm_mode

2006-08-14 Thread Naser, Md Abu
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] comm-mode = Angular

2006-04-26 Thread Naser, Md Abu
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)

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

2006-04-26 Thread Naser, Md Abu
+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

[gmx-users] comm-mode = Angular

2006-04-25 Thread Naser, Md Abu
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] distance measurement

2006-03-30 Thread Naser, Md Abu
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] distance measurement

2006-03-30 Thread Naser, Md Abu
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

[gmx-users] Decabe density

2006-03-23 Thread Naser, Md Abu
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