[gmx-users] force field for Titanium

2013-09-25 Thread mohammad agha
Dear Gromacs Specialists, I am searched force field for Titanium (Ti) element. Parameters consist of sigma and epsilon. Can you help me, Please? Best Regards Sara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive

Re: [gmx-users] force field for Titanium

2013-09-25 Thread mohammad agha
Thank you very much from your answer. Best Regards Sara From: Justin Lemkul jalem...@vt.edu To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, September 25, 2013 3:07 PM Subject: Re: [gmx-users] force

[gmx-users] old and new versions of gromacs

2013-07-20 Thread mohammad agha
Dear Gromacs Specialists I already worked with Gromacs-4.5.4. In the Gromacs site has been released new several versions. Has the old version (4.5.4) defects? Or are the new versions more complete? I want to continiue my simulations with 4.5.4, are there problems for it? I compared the manual

[gmx-users] old and new versions of gromacs

2013-07-20 Thread mohammad agha
Dear Gromacs Specialists I already worked with Gromacs-4.5.4. In the Gromacs site has been released new several versions. Has the old version (4.5.4) defects? Or are the new versions more complete? I want to continiue my simulations with 4.5.4, are there problems for it? I compared the manual

[gmx-users] old and new versions of gromacs

2013-07-20 Thread mohammad agha
Dear Justin, Thank you very much from your response. Best Regards Sara From: Justin Lemkul jalem...@vt.edu To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, July 20, 2013 3:47 PM Subject: Re: [gmx

[gmx-users] Fw: probability from COM of micelle

2013-05-13 Thread mohammad agha
- Forwarded Message - From: Justin Lemkul jalem...@vt.edu To: mohammad agha mra...@yahoo.com Cc: Sent: Monday, May 13, 2013 4:11 PM Subject: Re: probability from COM of micelle It is much better to post this information to the list so that others can benefit from it. -Justin On 5

[gmx-users] g_dist

2013-05-12 Thread mohammad agha
Dear GROMACS Specialists, I want to obtain number of instances the different atoms was found within a spherical shell of width 0.02 nm at a distance r from the micelle COM. For this, I use g_dist -dist, but when I select for example 0.04, it also result all instances in 0-0.02, whereas I want

[gmx-users] probability from COM of micelle

2013-05-10 Thread mohammad agha
to take into account the (average) volume of the simulation cell and the mass of the atom group to obtain the rho(r) (g.cm-3) as function of the Micelle COM otherwise, you will obtain the N(r) as function of Micelle COM (in nm-1) HTH On 5/9/13 10:15 AM, mohammad agha wrote: Dear GROMACS

[gmx-users] probability from COM of micelle

2013-05-10 Thread mohammad agha
to take into account the (average) volume of the simulation cell and the mass of the atom group to obtain the rho(r) (g.cm-3) as function of the Micelle COM otherwise, you will obtain the N(r) as function of Micelle COM (in nm-1) HTH On 5/9/13 10:15 AM, mohammad agha wrote: Dear GROMACS

[gmx-users] g_dist

2013-05-10 Thread mohammad agha
Dear GROMACS Specialists, I have one problem with g_dist. When I use g_dist along with option -dist, the output is printed on the terminal, but I want them into a file as separately. May I ask you to help me, Please? Thank you in advance Best Regards Sara -- gmx-users mailing list

[gmx-users] g_dist

2013-05-10 Thread mohammad agha
Dear Justin, Thank you very much from your answer. May I ask you to help me more, Please? I work with UBUNTU, I don't know how should I do it! Best Regards Sara On 5/10/13 11:27 AM, mohammad agha wrote: Dear GROMACS Specialists, I have one problem with g_dist. When I use g_dist along

[gmx-users] g_dist

2013-05-10 Thread mohammad agha
Dear Justin, Thank you very much from your help. Best Regards Sara On 5/10/13 11:27 AM, mohammad agha wrote: Dear GROMACS Specialists, I have one problem with g_dist. When I use g_dist along with option -dist, the output is printed on the terminal, but I want them into a file

[gmx-users] Fw: probability from COM of micelle

2013-05-09 Thread mohammad agha
Dear GROMACS Specialist, I want to plot probability (nm^-1) distribution of micelle selected atoms with respect to COM of the micelle (nm). with respect to this definition, Probability was defined as the number of instances the selected atom was found within a spherical shell of width 0.02 nm

[gmx-users] probability from COM of micelle

2013-05-09 Thread mohammad agha
Dear GROMACS Specialists, Thank you very much from your answer, but I want to know plotting this curve from g_rdf. May I ask you to give me one formula by this command, Please? Best Regards Sara On 2013-05-09 20:15, Justin Lemkul wrote: On 5/9/13 10:15 AM, mohammad agha wrote: Dear

[gmx-users] g_rdf

2013-03-30 Thread mohammad agha
Dear Gromacs Specialists, I want to find information about RDF of some components in my system but when I do the g_rdf command, I find true answers about RDF diagrams but my system type below note in several times: There were 2 inconsistent shifts. Check your topology May I know that this

[gmx-users] enough time for simulation

2013-01-07 Thread mohammad agha
Dear GROMACS Specialists, I have one system consists of many surfactant molecules that they create several micelles. How should I know that time of simulation is enough or not? that means where is the enough time for equilibrium of system? To creation of micelles, the small oligomers are merged

[gmx-users] equilibrium state

2012-12-24 Thread mohammad agha
Dear GROMACS Specialists, We know that one system is at equilibrium state when the variation of Helmholtz or Gibbs free energy be zero. May I ask you say me that how I can understand that my system has reached to equilibrium state in the end of simulation, Please? Best Regards Sara --

[gmx-users] Gibbs free energy

2012-12-24 Thread mohammad agha
Dear GROMACS Users, I work with NPT ensemble. Is the total energy equal to Gibbs free energy? Thanks in advance. Sara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at

[gmx-users] Gibbs free energy

2012-12-24 Thread mohammad agha
...@gmail.com To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, December 25, 2012 2:26 AM Subject: Re: [gmx-users] Gibbs free energy Obviosuly not. Total energy in MD = total potential energy + total kinetic energy. Read basis of MD

[gmx-users] Gibbs free energy

2012-12-24 Thread mohammad agha
Dear Steven, Many thanks from your help. In the manual at the section g_energy has been written that the gromacs calculate the delta G as is follows: Delta G = G(N,p,T) - G idgas(N,p,T) = kT ln eˆ(Upot/kT) But I don't understand why Upot? to calculate of delta S, I know that delta S =

[gmx-users] free energy

2012-12-23 Thread mohammad agha
Dea GROMACS Users, I want to calculate the free energy for my system, for example (Gibbs and Helmholtz), but I didn't define the free_energy in the md.mdp and my simulation has been finished!!! May I ask you that say me is there a solution fro this problem? Best Regards Sara -- gmx-users

[gmx-users] results of md

2012-12-04 Thread mohammad agha
Dear Gromacs Specialists, I ran one system (to create of micelles) tow times. Time of creation of micelles was different in each run and for example if it has been created 5 micelles (in the end of simulation) in both of them but the number of molecules presence in micelles (aggregation

[gmx-users] results of md

2012-12-04 Thread mohammad agha
and it is opposite of experimental results. Can you help me about this problem, Please? Best Regards Sara - Original Message - From: Justin Lemkul jalem...@vt.edu To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Wednesday, December 5, 2012

[gmx-users] about equilibrium

2012-10-15 Thread mohammad agha
Dear Gromacs Users, I have one system consists of: surfactant, solvent and additives. I made one box with only solvent and one box with only additives and equilibrated them little separable for better placing into the box, and then made one box with surfactant and then placed box of

[gmx-users] about equilibrium

2012-10-15 Thread mohammad agha
that equilibrate totally, there are not previous problems and I wanted to know that this method is correct? Best Regards Sara From: Justin Lemkul jalem...@vt.edu To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday

[gmx-users] about equilibrium

2012-10-15 Thread mohammad agha
Regards Sara - Original Message - From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Friday, October 5, 2012 9:34 AM Subject: Re: [gmx-users] equilibrium for box of simulation On 5/10/2012 3:55 PM, mohammad agha wrote: Dear

[gmx-users] about equilibrium

2012-10-15 Thread mohammad agha
Dear Justin, Thank you very much from your time. Best Regards Sara - Original Message - From: Justin Lemkul jalem...@vt.edu To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Monday, October 15, 2012 9:54 PM Subject: Re: [gmx-users

[gmx-users] equilibrium

2012-10-14 Thread mohammad agha
Dear Gromacs Users, I have one system consists of: surfactant, solvent and additives. I made one box with only solvent and one box with only additives and equilibrated them little separable for better placing into the box, and then made one box with surfactant and then placed box of solvent

[gmx-users] equilibrium

2012-10-14 Thread mohammad agha
Dear Gromacs Users, I have one system consists of: surfactant, solvent and additives. I made one box with only solvent and one box with only additives and equilibrated them little separable for better placing into the box, and then made one box with surfactant and then placed box of

[gmx-users] equilibrium

2012-10-14 Thread mohammad agha
Dear Gromacs Users, I have one system consists of: surfactant, solvent and additives. I made one box with only solvent and one box with only additives and equilibrated them little separable for better placing into the box, and then made one box with surfactant and then placed box of solvent

[gmx-users] equilibrium for box of simulation

2012-10-05 Thread mohammad agha
: Sent: Friday, October 5, 2012 9:34 AM Subject: Re: [gmx-users] equilibrium for box of simulation On 5/10/2012 3:55 PM, mohammad agha wrote: Dear Justin, Thank you very much. So, decreasing of box dimensions is not bad, if all thing process natural, yes? The cause of my doubt was because

[gmx-users] equilibrium for box of simulation

2012-10-05 Thread mohammad agha
/10/2012 4:12 PM, mohammad agha wrote: Dear Mark, Yes, you're right. Excuse me, for this and thank you for your reminder. May I know your idea about cause of my doubt, Please? As I said yesterday: At least one of your volume, contents or model physics are not consistent with the others

[gmx-users] equilibrium for box of simulation

2012-10-04 Thread mohammad agha
Dear GROMACS Users, I asked this question before but I don't understand it! I placed several materials in my box of simulation for example box with 6nm*6nm*6nm and my materials are not placed in the smaller box but when I equilibrate my system, the box became smaller and temperature and

[gmx-users] equilibrium for box of simulation

2012-10-04 Thread mohammad agha
and it is natural? Best Regards Sara - Forwarded Message - From: Justin Lemkul jalem...@vt.edu To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Thursday, October 4, 2012 5:52 PM Subject: Re: [gmx-users] equilibrium for box of simulation

[gmx-users] equilibrium for box of simulation

2012-10-04 Thread mohammad agha
: Sent: Thursday, October 4, 2012 5:48 PM Subject: Re: [gmx-users] equilibrium for box of simulation On 5/10/2012 12:06 AM, mohammad agha wrote: Dear GROMACS Users, I asked this question before but I don't understand it! I placed several materials in my box of simulation for example box

[gmx-users] equilibrium for box of simulation

2012-10-04 Thread mohammad agha
Message - From: Justin Lemkul jalem...@vt.edu To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Thursday, October 4, 2012 7:01 PM Subject: Re: equilibrium for box of simulation Please keep the discussion on the gmx-users list. On 10/4/12 11:28

[gmx-users] equilibrium for box of simulation

2012-10-04 Thread mohammad agha
the report of decreasing of box dimensions! May I know your idea about it, Please? Best Regards Sara - Original Message - From: Justin Lemkul jalem...@vt.edu To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Thursday, October 4

[gmx-users] g_clustsize

2012-09-27 Thread mohammad agha
Dear Gromacs users I have one big problem with g_clustsize! I see 9 micelles in my system after running. When I use g_clustsize for number of clusters and average cluster size, they don't emphasize each other, and I see 9 micelles from 36 ps to 120 ps in my box, but results of

[gmx-users] diffusion

2012-09-21 Thread mohammad agha
Desr Gromacs Users, I have several systems consist of: surfactants, solvent, and additives molecules in several concentrations. I want obtain extent of movement each of materials in the mixture in different concentrations. Is the self-diffusion coefficient good foe this? I have doubt about

[gmx-users] v-rescale

2012-09-18 Thread mohammad agha
Dear Gromacs Users, I have doubt about temperature bath coupling (v-rescale). I use this method (v-rescale) for my system, and my system is NPT ensemble. Has it problem? is v-rescale just used for NVT ensemble or it doesn't have restriction? Please help me. Thank you in advance Best Regards

[gmx-users] parameters for output control

2012-08-21 Thread mohammad agha
control On 21/08/2012 2:55 PM, mohammad agha wrote: Dear Justin, Thank you very much from your response. Yes, I said bad!!! My question is: For example, when I select -b 8 and Gromacs reads as (in the last step of reading from output file): Reading frame 13000 time 860040.000 , does

[gmx-users] parameters for output control

2012-08-20 Thread mohammad agha
Dear Gromacs Users, I have one problem about the way of computation in the Gromacs with frame and time. (I work with MARTINI CG) I have one md.mdp file that the parameters of output control in it is as follows: nsteps = 3000 dt = 0.030 ; Output control nstxout = 2000 nstvout = 2000

[gmx-users] parameters for output control

2012-08-20 Thread mohammad agha
or not? or does Gromacs perform the computations untill end of simulation (90 ps) and only doesn't printe in the command line? Best Reagrds Sara  - Original Message - From: Justin Lemkul jalem...@vt.edu To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users

[gmx-users] box of simulation

2012-08-15 Thread mohammad agha
Dear Mark, Unfortunately, my problem about box of simulation has not been solved! My command lines are as follow: 1- genbox -ci solute.gro -nmol 150 -box 12 12 12 -o solute150.gro 2- editconf -f solute150.gro -o solute1501.gro -c -d 1.0 -bt cubic -box 13.6 13.6 13.6 -center 6.8 6.8 6.8 3-

[gmx-users] box of simulation

2012-08-15 Thread mohammad agha
Dear Mark, Unfortunately, my problem about box of simulation has not been solved! My command lines are as follow: 1- genbox -ci solute.gro -nmol 150 -box 12 12 12 -o solute150.gro 2- editconf -f solute150.gro -o solute1501.gro -c -d 1.0 -bt cubic -box 13.6 13.6 13.6 -center 6.8 6.8 6.8 3-

[gmx-users] box of simulation

2012-08-15 Thread mohammad agha
/08/2012 10:27 PM, mohammad agha wrote: Dear Mark, Unfortunately, my problem about box of simulation has not been solved! My command lines are as follow: 1- genbox -ci solute.gro -nmol 150 -box 12 12 12 -o solute150.gro 2- editconf -f solute150.gro -o solute1501.gro -c -d 1.0 -bt cubic

[gmx-users] box of simulation

2012-08-14 Thread mohammad agha
Dear Gromacs Users: When I want to place 12000 solvent  molecule in the box (15*15*15)  it say: number of coordinates in coordinate file (ctacyc.gro, 28794) does not match topology (topol.top, 37950) it means that I should enlarge the box to place all of solvent molecules into that.

[gmx-users] box of simulation

2012-08-14 Thread mohammad agha
Dear Gromacs Users: When I want to place 12000 solvent  molecule in the box (15*15*15)  it say: number of coordinates in coordinate file (ctacyc.gro, 28794) does not match topology (topol.top, 37950) it means that I should enlarge the box to place all of solvent molecules into

[gmx-users] box of simulation

2012-08-14 Thread mohammad agha
Hi Emanuel, Thank you very much from your response. It means that it isn't one problem and it is natural.yes? Best Regards Sara - Original Message - From: Emanuel Birru emanuel.bi...@monash.edu To: 'mohammad agha' mra...@yahoo.com; 'Discussion list for GROMACS users' gmx-users

[gmx-users] Fw: box of simulation

2012-08-14 Thread mohammad agha
- Original Message - From: Emanuel Birru emanuel.bi...@monash.edu To: 'mohammad agha' mra...@yahoo.com; 'Discussion list for GROMACS users' gmx-users@gromacs.org Cc: Sent: Tuesday, August 14, 2012 12:06 PM Subject: RE: [gmx-users] box of simulation Hi Sara, The number of molecules

[gmx-users] box of simulation

2012-08-14 Thread mohammad agha
Thank you very much. Best Regards Sara - Original Message - From: Emanuel Birru emanuel.bi...@monash.edu To: 'mohammad agha' mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, August 14, 2012 12:46 PM Subject: RE: [gmx-users] Fw: box

[gmx-users] box of simulation

2012-08-14 Thread mohammad agha
://www.gromacs.org/Documentation/Terminology/Equilibration?highlight=equilibration http://www.gromacs.org/Documentation/Terminology/Pressure_Coupling Cheers, EB -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of mohammad agha Sent

[gmx-users] box of simulation

2012-08-14 Thread mohammad agha
/2012 6:55 PM, mohammad agha wrote: Dear Mark, Thank you very much from your help. I used from genbox to place solvent molecules. my question is : In the NPT ensemble, for equilibrium, may the box become smaller than definite sizes before equilibrium(for example 2nm become smaller) Yes

[gmx-users] g_clustsize

2012-07-24 Thread mohammad agha
Dear Gromacs Users, I don't know what is the quantity of -cut in g_clustsize for different systems, exactly! May I ask you to help me, Please? Best Regards Sara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages

[gmx-users] g_clustsize

2012-07-19 Thread mohammad agha
Dear Gromacs Users, I have several questions about g_clustsize, Please help me. I have several micelles in my system and I want to calculate: the number of monomers in micelles and cluster number and monomer number during the time of simulation, I used from this command as is follows:

[gmx-users] g_clustsize

2012-07-19 Thread mohammad agha
Dear Gromacs Users, I have several questions about g_clustsize, Please help me. I have several micelles in my system and I want to calculate: the number of monomers in micelles and cluster number and monomer number during the time of simulation, I used from this command as is follows:

[gmx-users] g_clustsize

2012-07-19 Thread mohammad agha
Dear Justin, Thank you very much from your response. according you said I should set -cut with less than 0.7, but this doesn't answer me! for 0.6: 0.00e+00 115   6.00e+01 107   1.20e+02 114   1.80e+02 105   2.40e+02 100   3.00e+02   

[gmx-users] g_clustsize

2012-07-19 Thread mohammad agha
Dear Justin, Thank you very much from your help. I think that I should work more on this command and will ask you next. I don't know why does it bother me for it's .xvg and -tu !!! Thank you very much again. Best Regards Sara On 7/19/12 9:42 AM, mohammad agha wrote: Dear Justin, Thank

[gmx-users] ngmx

2012-05-07 Thread mohammad agha
Dear Gromacs users, I work with Gromacs in Linux, I want prepare a copy of snapshots by ngmx with jpg or pdf format or whatever that be open in Windows. May I ask you to help me,Please? Best Regards Sara -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] ngmx

2012-05-07 Thread mohammad agha
From: Justin A. Lemkul jalem...@vt.edu To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Monday, May 7, 2012 10:28 PM Subject: Re: [gmx-users] ngmx On 5/7/12 1:50 PM, mohammad agha wrote: Dear Gromacs users

[gmx-users] ngmx

2012-05-07 Thread mohammad agha
Dear Justin, Thank you very much from your response. Best Regards Sara From: Justin A. Lemkul jalem...@vt.edu To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, May 8, 2012 6:15 AM Subject: Re: [gmx

[gmx-users] interface

2012-02-22 Thread mohammad agha
-users-boun...@gromacs.org] On Behalf Of mohammad agha Sent: Wednesday, 22 February 2012 3:12 AM To: Discussion list for GROMACS users Subject: [gmx-users] interface   Dear Gromacs Specialists,   I made a box consists of water with box lengths:  6nm  * 6nm  * 6nm , then I equilibrated it with NPT

[gmx-users] interface

2012-02-22 Thread mohammad agha
On 22/02/2012 3:11 AM, mohammad agha wrote: Dear Gromacs Specialists, I made a box consists of water with box lengths:  6nm  * 6nm  * 6nm , then I equilibrated it with NPT ensemble, box size increased to 6.66176, then I kept the x- and y-dimensions fixed, and double the system size in z

[gmx-users] interface

2012-02-22 Thread mohammad agha
/2012 10:34 PM, mohammad agha wrote: Dear Mark, Thank you very much from your reply. I see a box that the half of it consists of water and another half of box is void, but when I run md.mdp for production simulation all of water molecules dispersed in total of box and I don't see interface

[gmx-users] air-water interface

2012-02-21 Thread mohammad agha
Dear Gromacs Specialists, I want to make a system consists of one box of solvent (for example water) that there is 100 surfactant molecules in it and water is in contact with air in surface as same as we do in laboratory in beaker. But I don't know how should I define this air-water interface

[gmx-users] interface

2012-02-21 Thread mohammad agha
Dear Gromacs Specialists, I made a box consists of water with box lengths:  6nm  * 6nm  * 6nm , then I equilibrated it with NPT ensemble, box size increased to 6.66176, then I kept the x- and y-dimensions fixed, and double the system size in z as following: editconf -f pr1.gro -o newbox1.gro

[gmx-users] beads in martini

2012-02-04 Thread mohammad agha
Dear Specialist Gromacs, I want to compare properties of two micelles of different surfactants by MARTINI coarse-grained force field. The difference of these surfactants is in their counterion, one of them has bromide (Br-) ion and another has Chloride (Cl-). I know that I should show this

[gmx-users] g_rdf

2012-02-02 Thread mohammad agha
problem begins to resemble a nail.   From:gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of mohammad agha Sent: Thursday, 2 February 2012 3:48 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_rdf   Dear Prof. Thank you very much from your reply

Re: [gmx-users] g_rdf

2012-02-01 Thread mohammad agha
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of mohammad agha Sent: Tuesday, 31 January 2012 7:26 PM To: gmx-users@gromacs.org Subject: [gmx-users] g_rdf   Dear Prof.   I am confused about generation a radial density graph (density vs distance from center of mass), I know that I should use g_rdf

[gmx-users] g_rdf

2012-01-31 Thread mohammad agha
Dear Prof. I am confused about generation a radial density graph (density vs distance from center of mass), I know that I should use g_rdf. Then I count the number of atoms in the shells around the COM of special group by trjorder -com -nshell -r , next I use from this formula for compute

[gmx-users] g_rdf

2012-01-31 Thread mohammad agha
- Forwarded Message - From: mohammad agha mra...@yahoo.com To: gmx-users@gromacs.org gmx-users@gromacs.org Sent: Tuesday, January 31, 2012 11:56 AM Subject: g_rdf Dear Prof. I am confused about generation a radial density graph (density vs distance from center of mass), I know

[gmx-users] table potential

2012-01-20 Thread mohammad agha
Dear Gromacs users, I want to work by walls as table with martini coarse-grained. Is there anyone to help me for building table.xvg for bonds, angles and dihedrals in martini when I change vdw_type from shift to user? Thank you in advance. Best Regards Sara -- gmx-users mailing list

[gmx-users] walls

2012-01-17 Thread mohammad agha
Dear Gromacs users, May I ask you to help me about use of walls in martini coarse-grained, please? I defined two walls for my system as following: pbc        = xy         nwall  = 2 wall_type    = 12_6 wall_r_linpot    = 1 wall_atomtype = W  W I

[gmx-users] walls in martini

2012-01-16 Thread mohammad agha
Dear Prof. I want to use walls (in z=0 and z=z_box) for my simulation with martini coarse-grained force field, but always it give me error! Do the martini force field support walls? Should I use just 12-6 for wall_type? May I ask your help about this, Please? Best regards Sara-- gmx-users

[gmx-users] beads in martini corse-grained

2012-01-13 Thread mohammad agha
Dear Prof. I don't know about definition of sulfuric acid in Martini Corse-Grained, May I ask you to help me, Please? And Please say me about my definition of aniline as SC4, SC4, SNd that is correct? Best Regards Sara -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] xtcrev.py script

2012-01-11 Thread mohammad agha
Dear prof. I used a piece of python code that reverses a trajectory named xtcrev.py ((c)2011 Tsjerk A. Wassenaar), I have one problem when I ran it as following: ./xtcrev.py 1a.xtc 1a-rev.xtc it's error is: Traceback (most recent call last):   File ./xtcrev.py, line 54, in module     n   = 92

Re: Fw: [gmx-users] trjconv in martini

2012-01-11 Thread mohammad agha
? Best Regards Sara From: Tsjerk Wassenaar tsje...@gmail.com To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, January 11, 2012 12:54 PM Subject: Re: Fw: [gmx-users] trjconv in martini Hi Sara, That can

Re: Fw: [gmx-users] trjconv in martini

2012-01-11 Thread mohammad agha
and thank you very much but may I ask you any suggestion about my problem, please? Best Regards Sara rom: Tsjerk Wassenaar tsje...@gmail.com To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, January

Re: Fw: [gmx-users] trjconv in martini

2012-01-11 Thread mohammad agha
Hi Tsjerk, I have a good news!!! That was corrected!!! Thank you very much from your help. Best Regards Sara From: Tsjerk Wassenaar tsje...@gmail.com To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent

[gmx-users] aniline beads

2012-01-11 Thread mohammad agha
Dear Gromacs users, I defined tree beads for aniline consists of SC4, SC4 and SNd as following: [moleculetype] ; molname     nrexcl   DRG         1 [atoms] ; id     type     resnr     residu     atom     cgnr     charge   1 SNd 1   DRG NH2     1   0   2     SC4     1     DRG 

Re: Fw: [gmx-users] trjconv in martini

2012-01-10 Thread mohammad agha
From: Tsjerk Wassenaar tsje...@gmail.com To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, December 31, 2011 3:41 PM Subject: Re: Fw: [gmx-users] trjconv in martini Hi Sara, # Extract the first part

Fw: Fw: [gmx-users] trjconv in martini

2012-01-10 Thread mohammad agha
- Forwarded Message - From: mohammad agha mra...@yahoo.com To: gmx-users@gromacs.org gmx-users@gromacs.org Sent: Tuesday, January 10, 2012 9:08 PM Subject: Re: Fw: [gmx-users] trjconv in martini Hi Tsjerk, I know that my question is silly but please help me. I installed python2.5

Re: Fw: [gmx-users] trjconv in martini

2011-12-31 Thread mohammad agha
Hi Tsjerk, Thanks for your reply, yas, I did this too! Best Regards Sara From: Tsjerk Wassenaar tsje...@gmail.com To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, December 31, 2011 11:42 AM Subject

Re: Fw: [gmx-users] trjconv in martini

2011-12-31 Thread mohammad agha
Hi Tsjerk, Thanks for your reply, yes, I did this, too! but my problem wasn't solved! Best RegardsSara From: Tsjerk Wassenaar tsje...@gmail.com To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday

Re: Fw: [gmx-users] trjconv in martini

2011-12-31 Thread mohammad agha
workflow. I hope work this time. I thank you very very much again. Best Regards Sara From: Tsjerk Wassenaar tsje...@gmail.com To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, December 31, 2011 2:18 PM

Re: Fw: [gmx-users] trjconv in martini

2011-12-31 Thread mohammad agha
Hi Tsjerk, Thank you very much from your help. Best Regards Sara From: Tsjerk Wassenaar tsje...@gmail.com To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, December 31, 2011 3:41 PM Subject: Re: Fw

[gmx-users] trjconv in martini

2011-12-30 Thread mohammad agha
Dear gromacs users, At the first I thank from Tsjerk and Mark because of their answers to me but unfortunately I don't understand that where is my mistake, still? I work with MARTINI coarse-grained and I have a problem after -pbc nojump! My simulation lasts 600 ns and 2 micelles are created

Fw: [gmx-users] trjconv in martini

2011-12-30 Thread mohammad agha
- Forwarded Message - From: mohammad agha mra...@yahoo.com To: Tsjerk Wassenaar tsje...@gmail.com Sent: Friday, December 30, 2011 3:16 PM Subject: Re: [gmx-users] trjconv in martini Hi Tsjerk, Thank you very much from your reply, I have a problem about ./xtcrev.py 1a.xtc 1a

Re: Fw: [gmx-users] trjconv in martini

2011-12-30 Thread mohammad agha
Hi Tsjerk, Thank you for your reply, yes it is #!/usr/bin/env python May I ask you to help me? Best Regards Sara From: Tsjerk Wassenaar tsje...@gmail.com To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent

[gmx-users] trjconv -nojump

2011-12-28 Thread mohammad agha
- Forwarded Message - From: mohammad agha mra...@yahoo.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, December 27, 2011 8:59 PM Subject: Re: [gmx-users] trjconv and g_clustsize Thank you very much from your reply. I found out that my problem

[gmx-users] -pbc nojump

2011-12-28 Thread mohammad agha
Dear GROMACS users, I have a problem about trjconv -pbc nojump, I have 2 micelles in the end of my simulation. For analysis I should do three steps for micelle clustering at http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering?highlight=micelle+clustering  Steps 1 and 2 work good and

Re: [gmx-users] -pbc nojump

2011-12-28 Thread mohammad agha
Thank you very much from your reply. Best Regards Sara From: Tsjerk Wassenaar tsje...@gmail.com To: mohammad agha mra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, December 29, 2011 1:56 AM Subject: Re: [gmx-users] -pbc

Re: [gmx-users] trjconv and g_clustsize

2011-12-27 Thread mohammad agha
and g_clustsize On 12/26/2011 7:53 PM, mohammad agha wrote: Dear Prof. I have several questions about trjconv, please help me. In my simulation is created 2 micelles. 1- When I do 3 steps of micelle clustering as follows:   a- trjconv -f md.xtc -o a_cluster.gro-e 60 -pbc cluster  b- grompp -f

[gmx-users] trjconv and g_clustsize

2011-12-26 Thread mohammad agha
Dear Prof. I have several questions about trjconv, please help me. In my simulation is created 2 micelles. 1- When I do 3 steps of micelle clustering as follows:   a- trjconv -f md.xtc -o a_cluster.gro-e 60 -pbc cluster  b- grompp -f md.mdp -c a_cluster.gro -o a_cluster.tpr  c- trjconv -f

[gmx-users] micelle clustering

2011-12-24 Thread mohammad agha
Dear GROMACS users I want to analysis of 2 micelles that are created in one simulation, when I view output of trajectory by vmd or ngmx: ngmx -f md.trr -s md.tpr has been created 2 micelles, then I try to micelle clustering by: 1. trjconv -f md.xtc -o a_cluster.gro -e 0.001 -pbc

Re: [gmx-users] micelle clustering

2011-12-24 Thread mohammad agha
, mohammad agha wrote: Dear GROMACS users I want to analysis of 2 micelles that are created in one simulation, when I view output of trajectory by vmd or ngmx: ngmx -f md.trr -s md.tpr has been created 2 micelles, then I try to micelle clustering by: 1. trjconv -f md.xtc -o a_cluster.gro -e

[gmx-users] calculation of concentration

2011-12-22 Thread mohammad agha
Dear GROMACS users I doubt about calculate the concentration of my system. I know that concentration is calculated from the number of molecules / Avogadro’s number and divided by volume of box, but I think I calculate wrong, for example in one of articles had been written: 7579 water molecules

[gmx-users] pressure coupling

2011-12-16 Thread mohammad agha
Dear GROMACS Users I have a warning after doing pr.mdp as followed, I read errors in GROMACS site and checked mailing list, but my warning is only step1 and after that equilibration is run normally till end.  500 steps, 15.0 ps. step 0 Step 1  Warning: pressure scaling more than 1%,

Re: [gmx-users] pressure coupling

2011-12-16 Thread mohammad agha
From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Saturday, December 17, 2011 10:22 AM Subject: Re: [gmx-users] pressure coupling On 17/12/2011 5:40 PM, mohammad agha wrote: Thank you very much. Excuse me, I did

Re: [gmx-users] calculation of density for martini coarse-grained

2011-12-15 Thread mohammad agha
AM Subject: Re: [gmx-users] calculation of density for martini coarse-grained On 15/12/2011 5:59 PM, mohammad agha wrote: Dear Prof. May I ask you two questions, Please? 1- I work with MARTINI force field. I have a surfactant molecule consists of 5 beads. After I placed 151 surfactants

  1   2   >