> Thanks for your reply.
>
> I'm following the protocol of Diagnosing an unstable system. Corresponding
> the first step I changed th nstxout to 1 for 3 times.
> The first and second time I got error the same as before ( some interactions
> seem to be assigned multiple times ) and it the warning
I think your RMSD of 0.000539742 is quite a small value, which can be,
at least theoretically, caused by the accumulation of errors. Can you
simulate your protein for a longer time to show that RMSD is indeed
significant?
On Sat, Jul 28, 2012 at 1:01 AM,
wrote:
> Hi,
> my problem is, that duri
>
> I want to do a minimization and a md run with my protein. But I only want
> the hydrogen atoms to be minimized but not the rest of the protein.
> I use the
> freezegrps = Protein-H
> freezedim = Y Y Y
>
> option in my mdp files to make sure that they don't change.
>
> During the minimization st
> I have the following Notes during NPT equilibration.
>
> NOTE 1 [file pr_NPT.mdp]:
> nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
> nstcomm to nstcalcenergy
>
>
> NOTE 2 [file pr_NPT.mdp]:
> leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
>
> Dear All
> I want to obtain the instantaneous dipole moment as an output for the
> OH bond in the pure water molecule simulation.
> Given the conditions that most of the water models have fixed
> coordinates and charges during the course of simulation
> how can I get the same.Is there any pos
>
> I am trying to change all lipid acyl tails to a trans orientation, and
> thought that restraining all tail dihedrals to 180 should work quickest. I
> have also tried smaller angles (120, 100) and the effect is the same,
> leaflets drifting apart.
>
> In fact, the 180 restraint does work fine in
> I am trying to implement dihedral restraints for lipids in a bilayer
> using what is suggested here:
>
> http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints
>
> However, although the dihedral angles seem to be restrained fine, the
> leaflets move apart by 10s of nanometers along +z o
>> Dear GROMACS people -
>>
>> I am calculating radial distribution function between the centers of
>> mass of two large particles in a periodic box.
>>
>> My command is -- g_rdf_455 -n 2drops.ndx -rdf mol_com -s topol.tpr -f
>> conf.gro
>>
>> My index file contains two groups of atoms standing fo
> On 6/21/12 3:20 PM, Dr. Vitaly V. G. Chaban wrote:
>>
>> Dear All -
>>
>> I have a macromolecule surrounded by multiple layers of water in my
>> box. For visualization purposes, I would like to center the
>> macromolecule in the box (PDB file), so that i
Dear All -
I have a macromolecule surrounded by multiple layers of water in my
box. For visualization purposes, I would like to center the
macromolecule in the box (PDB file), so that its geometrical center
coincides with the geometrical center of the cubic box (as
visualization utilities undertan
>>>
>>> Does gmx provide any script to calculate autocorrelation function
>>> for a defined bond (not hydrogen bond autocorrelation function,g_hbond) ?
>>>
>>> Thanks a lot for the information!
>>
>>
>> Assuming that you mean the aucorrelation function (ACF) of the bond
>> length fluctuations aroun
> Hello
>
> Does gmx provide any script to calculate autocorrelation function
> for a defined bond (not hydrogen bond autocorrelation function,g_hbond) ?
>
> Thanks a lot for the information!
Assuming that you mean the aucorrelation function (ACF) of the bond
length fluctuations around its equili
12 matches
Mail list logo
