[gmx-users] COM motion removal

Dear Gromacs users!! I have a lipid - peptide system which I simulated for 50ns. Now in the beginning of the simulation the peptide was at the center of the bilayer but with time the peptide moved and came very close to the edge. Now near the edge it is having the interactions with the images o

Re: [gmx-users] translation

ussion list for GROMACS users Sent: Tuesday, 12 August, 2008 1:15:00 AM Subject: Re: [gmx-users] translation priyanka srivastava wrote: > Dear Justin, > > Thanks a lot for replying back. > > These are the two things that I have tried but still the peptide does > not co

Re: [gmx-users] translation

.. - Original Message From: Justin A. Lemkul <[EMAIL PROTECTED]> To: Discussion list for GROMACS users Sent: Tuesday, 12 August, 2008 12:05:26 AM Subject: Re: [gmx-users] translation priyanka srivastava wrote: > Dear All, > > I really apologize for asking a peptide trans

[gmx-users] translation

Dear All, I really apologize for asking a peptide translation related question again. I have a lipid-peptide system and I have already carried out the production run for 20ns. The peptide has moved towards one of the edges (I didnt specify comm-grps in the mdp file). I have to translate the pep

[gmx-users] ACE patch in FFG43a1

Dear All, I have a problem when I use ACE patch in one of my proteins using FFG43a1. I am issuing: pdb2gmx_3.3 -f test.pdb -ter -ignh -o test.gro I am using -ter because I already have ACE at N terminus and NH2 at C-terminus. I used this test.gro and put it in a water box and went ahead with e

[gmx-users] peptide translation

Dear All, I have a lipid - peptide system and while running the production run I forgot to assign comm-grps, thus the peptide has actually shifted from the center towards one of the edges. I have searched the forum and tried all possible options in trjconv i.e. -center zero, -fit translation, p

Re: [gmx-users] comm_grps

In the end it might, however, not make a big difference... Jochen priyanka srivastava wrote: > Dear All, > > I am a little confused with the application of > comm_grps. I have a lipid-peptide system in which I am > using the default values i.e. > > comm_mode: linear > n

[gmx-users] comm_grps

Dear All, I am a little confused with the application of comm_grps. I have a lipid-peptide system in which I am using the default values i.e. comm_mode: linear nstcomm: 1 comm_grps: whole system Is there something wrong with defining comm_grps = whole system for the lipid-peptide case? Is it ne

[gmx-users] density profile of bilayers

Dear all, I wish to calculate the density profile of a lipid bilayer i.e the electron density and this is how I am using the g_density command: g_density -f final.trr -s final.tpr -ei electrons.dat -o density.xvg -ed -symm where electrons.dat contains # of electrons information for each and eve

[gmx-users] Surface Tension units

Dear All, I have carried out an analysis of the surface tension value of a bilayer system. I wish to know what are the units of surface tension and is it calculated as "per interface" or for the entire bilayer (including two leaflets). waiting for the reply eagerly, Priyanka S. _

Re: [gmx-users] A very Basic query

t; system ("g_dist << EOF > > 13 > > 14 > > EOF"); > > $i=$i+1; > > } > > > > Venky > > > > On Aug 22, 2007, at 7:44 AM, priyanka srivastava > wrote: > > > >> Dear All, >

[gmx-users] A very Basic query

Dear All, Apologies for a very basic query. I wish to run g_dist command using groups 13 & 14 say 10 times, when I write the perl script it prompts me at the following point 10 times: Select a group: So I have to manually give 13 and 14 each time. Is there anyway in gromacs to automate it??

Re: [gmx-users] lipid simulations

I too feel that Chris's reply was indeed very very elaborative and written in such a fine way that you would not find it written like this in any manual or papers/research articles. I too am into lipid simulations and I am thankful to Chris for such a clear and nice response. I think, it is of

[gmx-users] writing xtc file from trr file

Dear all, While running a job, since there was space problem I could not write the xtc files. Now when I do the analysis and use the trr file it reports the time values after every 5ps i.e. 2000, 2005, 2010 etc. However I wish to write the xtc file using trjconv such that the timestep is report

Re: [gmx-users] g_bundle!

original position. Pri... --- TJ Piggot <[EMAIL PROTECTED]> wrote: > use the program make_ndx or just edit the .ndx file > using a text editor > > Tom > > --On 21 June 2007 11:03 -0700 priyanka srivastava > <[EMAIL PROTECTED]> > wrote: > > > Doe

Re: [gmx-users] g_bundle!

lete turn of the backbone of the > helix at each end as possible. > Your output is not surprising, given what you've > asked the program for - the axis between two points > that precisely overlap ;-) > > - Original Message > From: priyanka srivastava <[EMAIL PR

Re: [gmx-users] Basic Query

= 1.5 > > Also since I have not specified "vdwtype" in the mdp > file, so it automatically takes Cut-off. > > regards, > Pri... > > > --- Martin H�fling wrote: > >> Am Mittwoch, 20. Juni 2007 schrieb priyanka >> srivastava: >>

Re: [gmx-users] Basic Query

: > Am Mittwoch, 20. Juni 2007 schrieb priyanka > srivastava: > > > I am currently involved in doing a lipid-peptide > > simulation under NPAT conditions. The way I have > > applied NPAT condition is as follows: > > > > ref_p =

[gmx-users] g_bundle!

Dear All, I want to calculate tilt angle of a peptide inserted inside the lipid bilayer (i.e. angle between the helical axis and bilayer normal). From previous posts I got an idea that g_bundle wud solve my problem. I am issuing the following on the command line: g_bundle -f test.xtc -s test.tpr

[gmx-users] Basic Query

Hie all, I am currently involved in doing a lipid-peptide simulation under NPAT conditions. The way I have applied NPAT condition is as follows: ref_p = 0 1 compressibility = 0.0 4.5e-5 Although while performing analysis it shows that the x and y dimensions are consta

Re: [gmx-users] combination rules

or a different one, or the one that is mentioned in chapter5. Also, this is specific to the [pairtypes] in lipid.itp. regards, Pri... --- Mark Abraham <[EMAIL PROTECTED]> wrote: > priyanka srivastava wrote: > > Dear All, > > > > I would be really thankful if someb

[gmx-users] combination rules

Dear All, I would be really thankful if somebody could tell me the combination rules used for creating the [pairtypes] in lipid.itp (i.e. the 1,4 interactions) in GROMOS96. Is it the same as is used in GROMOS87? eagerly waiting for the reply, regards, Pri...

[gmx-users] lipid.itp???

Subject: [gmx-users] scaling factor?? Hie people, Can somobody please tell me how the "paramaters for lipid-GROMOS interactions" in lipid.itp file has been scaled? warm regards, Pri... Sucker-punch sp

[gmx-users] scaling factor??

Hie people, Can somobody please tell me how the "paramaters for lipid-GROMOS interactions" in lipid.itp file has been scaled? warm regards, Pri... Finding fabulous fares is fun. Let Yahoo! FareChase searc

Re: [gmx-users] orthorhobmic box??

rs). thanks & regards, Priyanka S. --- Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: > Hi Priyanka, > > You also have to set the -angles between the > vectors. Otherwise > editconf assumes a rectangular box. > > Cheers, > > Tsjerk > > On 2/27/07,

Re: [gmx-users] orthorhobmic box??

angles : 90.00 90.00 90.00 (degrees) box volume : 189.51 (nm^3) --- Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: > Hi Priyanka, > > You also have to set the -angles between the > vectors. Otherwise > editconf assumes a rectangular box. >

[gmx-users] orthorhobmic box??

Dear All, Is it correct to use the following command for generating an orthorhombic box? editconf -box x y z -f test.gro -o final.gro test.gro has (0 0 0) as box dimension whereas final.gro has (x y z) Eagerly waiting for response, Priyanka S.

[gmx-users] sigma-epsilon to c6-c12

Dear All, This might be a trivial question but please help me in converting the sigma/epsilon to c6/c12 parameters. How are they linked? thanks in advance, Priyanka. S. - Bored stiff? Loosen up... Download and play hundreds of games for free on Yaho

[gmx-users] membrane set up!!!

The below-mentioned lines (from forum) do not work for me!! I am dealing with DMPC instead of POPC and I hope that is not making any difference!! kindly help, Priyanka S. ""Hu Ugur, actually you don't have to care to run the lipid pdb by Tieleman through pdb2gmx at all - just copy the respectiv

[gmx-users] itp files in membrane simulation

Dear all, I want to use lipid.itp & dmpc.itp for a bilayer simulation, and I have gathered this information so far that one has to manually modify these itp files in order to use the latest force fields, ie, G43a2 etc. Does this include lipid.itp file too which involves various lipid-GROMOS inter

[gmx-users] surface tension

Dear all, what is the unit of surface tension in gromacs analysis? Is it dyn/cm or N/m. As according to me it is coming out to be in terms of N/m but it is attached with a conversion factor of some powers of 10. Kindly guide me. If I am getting e.g. 930.002 as the surface tension then what are it

Re: [gmx-users] g_order C code

ode. See > below. > > On Thu, 2006-09-14 at 04:44 -0700, priyanka > srivastava wrote: > > Thank you for your reply. > > > > I am also curious to know if this is the right way > of > > doing it. I am not sure of the changes that I have > > made in the cod

Re: [gmx-users] g_order C code

thanks and regards, Priyanka. --- Erik Marklund <[EMAIL PROTECTED]> wrote: > On Thu, 2006-09-14 at 02:21 -0700, priyanka > srivastava wrote: > > Dear Gromacs users, > > Hie, > > > > I am calculating the order parameters for a > bilayer > > pat

[gmx-users] g_order C code

Dear Gromacs users, Hie, I am calculating the order parameters for a bilayer patch using g_order analysis tool in gromacs version 3.3. I have a total of 48 elements in the patch and I want the order parameter value for each and every element i.e. a total of say 48 values for order parameter along

[gmx-users] g_order

Hie All, While using the tool g_order I am getting NAN (not a number), as is pasted below: Atom 4 Tensor: x=-0.229462 , y=-0.180263, z=0.409725 Atom 5 Tensor: x=nan , y=nan, z=nan Atom 6 Tensor: x=nan , y=nan, z=nan Atom 7 Tensor: x=-0.219508 , y=-0.176833, z=0.396342 Has anybody ever encountere

[gmx-users] NAN in g_order analysis!!

Dear All, While analysing one of the trr files using g_order I am getting two NANs (not a number) in the deuter.xvg and order.xvg between an interval of 1ns. (specified by using -b and -e command). what does this signify and why is this happening? Does this show that there is some problem with th

Re: [gmx-users] Is there any bug in gromacs v3.3 g_order analysis tool?

der Spoel <[EMAIL PROTECTED]> wrote: > priyanka srivastava wrote: > > Dear gromacs users, > > > > I am doing a lipid-bilayer simulation using > gromacs > > 3.3 version. While calculating the order > parameters, > > although I am having a hard time

[gmx-users] Is there any bug in gromacs v3.3 g_order analysis tool?

Dear gromacs users, I am doing a lipid-bilayer simulation using gromacs 3.3 version. While calculating the order parameters, although I am having a hard time. When I issue the following command: g_order -f lb.trr -s lb.tpr -n sn2.ndx -b 0 -e 30 I get the following output: trn version: GMX_trn_

[gmx-users] a question on the -sed, trjconv output & g_order

Dear Gromacs Users, I have a doubt related to the .gro file that I am extracting using: trjconv -f test.trr -o test.gro -b 0 -e 1000 -sep -s test.tpr I get the time pattern, a portion of which is like this in the files say from 0 to 1000ps: h 48 lipids and 1437 waters t= 85.1 h 48 lipids a

Re: [gmx-users] Gromacs 3.3 & g_order

Dear All, Sorry for bothering you all, I was doing some mistake while doing cat, it is working fine. sorry for the botheration, Pri... --- priyanka srivastava <[EMAIL PROTECTED]> wrote: > Dear All, > > I did a simulation of a lipid bilayer upto 10ns and > want to calculate i

[gmx-users] Gromacs 3.3 & g_order

Dear All, I did a simulation of a lipid bilayer upto 10ns and want to calculate its order parameter using g_order analysis tools. Since it was restarted in the middle so after the completion of 10ns I used cat command to combine the trr and tpr files to make one trr and tpr files for 10ns. Also, b

Re: [gmx-users] Kindly read this one, Apologies for the previous mail.

thank you so much for a prompt reply. how about the ref_p value? will that be 1 only? or 0 1 the way I had specified in my previous mail? regards, pri... --- Pedro Alexandre Lapido Loureiro <[EMAIL PROTECTED]> wrote: > > > > compressibility = 0 0 0 0 0 0 ; off diagonals are > zero > > > >

[gmx-users] Kindly read this one, Apologies for the previous mail.

Dear All, I want to do a lipid simulation using NPAT ensemble. This is how I am defining the .mdp file. I am not sure of these values though, kindly correct me if I am doing something wrong. compressibility = 0 0 0 0 0 0 ; off diagonals are zero too!(hence 6 value

[gmx-users] NPAT

Dear All, I want to do a lipid simulation using NPAT ensemble. This is how I am defining the .mdp file. I am not sure of these values though, kindly correct me if I am doing something wrong. compressibility = 0 0 0 0 0 0 ; off diagonals are zero too! ref_p 0 1 pcoupltype semiisotropic; requi

Re: [gmx-users] lipid order parameter

This reference is the one which reports sn2 but I am looking for sn1 as well. :-(   Pri...   [EMAIL PROTECTED] wrote: > Dear Gromacs users,> I am looking for individual experimental (NMR) order parameter > values for sn1 and sn2 chains at physiological temperature for DMPC > in order to carry

[gmx-users] lipid order parameter

Dear Gromacs users, I am looking for individual experimental (NMR) order parameter values for sn1 and sn2 chains at physiological temperature for DMPC in order to carry out the analysis of my trajectories and compare the results. I have got the values for sn-2 chain but unable to get it for sn1ch

Re: [gmx-users] atom names do not match

problem? thanks and regards, Pri... --- David van der Spoel <[EMAIL PROTECTED]> wrote: > priyanka srivastava wrote: > > Thanks again for your kind response. > > > > I guess I will write down my problem once again > :-) > > > > I am trying to study a

[gmx-users] atom names do not match

Thanks again for your kind response. I guess I will write down my problem once again :-) I am trying to study a pure bilayer system for which I am interested in running the production run using gromacs. I already have the system with me i.e. a pdb file after the minimization and all the constrai

[gmx-users] grompp

Thank you all for such a prompt reply :-) I am running grompp for a pure lipid system and grompp gives me the error that: number of coordinates in coordinate file (96_neatsys14.gro, 19926) does not match topology (96_neatsys14.top, 13014) I found out that the total 6912 atoms (19926-13014) that

[gmx-users] lipid .gro file

Dear All, I am trying to convert a pdb file containing all DMPC coordinates to .gro file. I have searched through the web and found out that I am not to use pdb2gmx directly and also that I have to make a .top file containing dmpc.itp and lipid.itp files. I am a beginner in gromacs so kindly hel