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
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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
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 (
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
I am trying to simulate mixture of DMSO and water at different mole
fractionbut this value is for 100% DMSO.
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Sent from the GROMACS Users Forum mailing list archive at Nabble
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
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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
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
Dear Users,
I am try to simulate DMSO molecules. I am getting potential energy values of
Energy Average Err.Est. RMSD Tot-Drift
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Potential -28160.8 4259.924
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
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
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
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:
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Program mdrun_d, VERSION 4.6.5
Source code file:
/users/khaos/prog/src/g
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
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:
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