[gmx-users] Calculating the displacement of an atom QUERY

2013-12-23 Thread rbbioinfo
Hi, I want to plot the total displacement of an atom/ion along Z axis with respect to time. Anybody kindly help me regarding how to calculate the movement of any atom using gromacs. An early response will be highly appreciated. Thanking you, Rajabrata -- View this message in context: http://grom

[gmx-users] N-H order parameter

2013-12-23 Thread Ahmet yıldırım
Dear users, g_chi computes "Dihedral Order Parameters". order.xvg: #Res. S2Min S2MaxPhiPsi Omega 1 0.000 0.873 0.000 0.873 0.000 2 0.463 0.853 0.463 0.783 0.853 3 0.476 0.889 0.731 0.47

Re: [gmx-users] MTTK with double precision GROMACS

2013-12-23 Thread Michael Shirts
MTTK with constraints has a tendency to fail with numerical stability issues. It is perfectly good as long as it doesn't fail. We will retire it in 5.1 or so. In the meantime, things that can reduce failures due to numerical instability. - Apply constraints only to h-bonds - make tau_p longer (

Re: [gmx-users] Potential energy calculations

2013-12-23 Thread Justin Lemkul
Gromacs reports energies in kJ per mole of equivalent systems. If you're looking for a value like configurational energy, use g_energy -nmol as needed to divide by the number of molecules in the system. -Justin On Mon, Dec 23, 2013 at 8:49 PM, virk wrote: > I am trying to simulate mixture of

Re: [gmx-users] Potential energy calculations

2013-12-23 Thread virk
I am trying to simulate mixture of DMSO and water at different mole fractionbut this value is for 100% DMSO. -- View this message in context: http://gromacs.5086.x6.nabble.com/Potential-energy-calculations-tp5013495p5013499.html Sent from the GROMACS Users Forum mailing list archive at Nabble

Re: [gmx-users] Potential energy calculations

2013-12-23 Thread virk
sorry, I didn't understand it what do you mean by zero it.But I have stabilised energy calculation for my simulation..I am thinking something wrong with units or something with my simulation -- View this message in context: http://gromacs.5086.x6.nabble.com/Potential-energy-calculati

Re: [gmx-users] Potential energy calculations

2013-12-23 Thread Robert Darkins
The potential energy of what exactly? The energy of bringing the atoms together to form a single DMSO molecule? If so then MD isn't appropriate for this type of calculation... On 24/12/13 00:33, virk wrote: Dear Users, I am try to simulate DMSO molecules. I am getting potential energy values

Re: [gmx-users] Potential energy calculations

2013-12-23 Thread lloyd riggs
Did you zero it ?   Stephan Watkins   Gesendet: Dienstag, 24. Dezember 2013 um 01:33 Uhr Von: virk An: gmx-us...@gromacs.org Betreff: [gmx-users] Potential energy calculations Dear Users, I am try to simulate DMSO molecules. I am getting potential energy values of Energy Average Err.Est. R

[gmx-users] Potential energy calculations

2013-12-23 Thread virk
Dear Users, I am try to simulate DMSO molecules. I am getting potential energy values of Energy Average Err.Est. RMSD Tot-Drift --- Potential -28160.8 4259.924

Re: [gmx-users] conversion of X,Y,Z + velocities to *.trr

2013-12-23 Thread Mark Abraham
On Mon, Dec 23, 2013 at 8:43 PM, Rasoul Nasiri wrote: > Thanks for your replies. > > 1- I need bond and charge info along with position and velocity ones. > All change during the MD simulation required a reactive force field rather > than > traditional one. > > 2- How one can construct a tpr for

Re: [gmx-users] polymer-topology generation

2013-12-23 Thread Justin Lemkul
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2009-March/040125.html -Justin On Mon, Dec 23, 2013 at 4:33 PM, decaiyu wrote: > Dear All,Can anyone help me find the link to the example to make polymer > residue files?The link below does not work on the website.Best > Regards,Deca

Re: [gmx-users] polymer-topology generation

2013-12-23 Thread decaiyu
Dear All,Can anyone help me find the link to the example to make polymer residue files?The link below does not work on the website.Best Regards,Decai Yu GROMACS is well-suited for running simulations of polymeric materials. One of the questions frequently asked on the gmx-users list is how to cre

[gmx-users] MTTK with double precision GROMACS

2013-12-23 Thread khaos
Dear all, I'm trying to run the DPPC bilayer simulation using the double precision GROMACS with the MTTK pressure coupling method. However, I've got an error like this: --- Program mdrun_d, VERSION 4.6.5 Source code file: /users/khaos/prog/src/g

Re: [gmx-users] conversion of X,Y,Z + velocities to *.trr

2013-12-23 Thread Rasoul Nasiri
Thanks for your replies. 1- I need bond and charge info along with position and velocity ones. All change during the MD simulation required a reactive force field rather than traditional one. 2- How one can construct a tpr for a system in which bonds/charges change when it's evolved? Best, Raso

Re: [gmx-users] conversion of X,Y,Z + velocities to *.trr

2013-12-23 Thread Tsjerk Wassenaar
Also, consider what you need it for. If you only need atom/residue information and/or reference coordinates, a .gro/.pdb file will do. Only if you need to have bonds/masses/charges/... you really need a .tpr file for reference. Cheers, Tsjerk On Mon, Dec 23, 2013 at 4:00 AM, Mark Abraham wrote: