Hi Alan,
I have no experience with acpypi, so I can't tell which one does better,
or why... rdparm not being needed, that would be a strong point.
Unfortunately, I'm running a bit short of time at the moment, so I can't
really spend a lot of time looking into unknown codes, hope you
Hi,
Right, the only dihedral angles that do not allow an exact translation to
RB because of the phase are the ones involving the new parametrization for
nucleic acids. Namely, it corrects the alpha/gamma transitions to get the
populations of states right, thus avoiding the loss of helicity on
Justin A. Lemkul wrote:
[EMAIL PROTECTED] wrote:
Hi everyone,
I'm having problems running an md simulation (with gmx-4.0.2) using vsites
and a time step of 4fs. I did generate the tpr with pdb2gmx. The problem
seems to occur when the molecule crosses pbc, since the first sign of the
--- Missatge original
Assumpte:
De: [EMAIL PROTECTED]
Data: Tue, Novembre 25, 2008 9:52 am
A:Discussion list for GROMACS users gmx-users@gromacs.org
[EMAIL PROTECTED]
Hi everyone,
As I wrote yesterday, I'm having problems running stable simulations with
vsites and constraints in all bonds in different time-steps using
gmx-4.0.2. As long as the dna strand does not cross pbc, the simulations
run fine (the longest I did was 5ns). The dna topology was generated
Hi everyone,
I'm having problems running an md simulation (with gmx-4.0.2) using vsites
and a time step of 4fs. I did generate the tpr with pdb2gmx. The problem
seems to occur when the molecule crosses pbc, since the first sign of the
simulation not working fine after ~3ns is
Warning: 1-4
Hi users,
I would like to restart some REMD simulations done with the cvs code with
the new checkpoint feature, but I'm unsure if I'm doing it right. Each
replica has its own state#.cpt file, but it seems to me that the -cpi
option of the cvs mdrun (at version 3.3.99_development_20080718) only
In the old version of gmx, and I think nobody changed a single line of
code, this is the message you would get regardless of the file you input.
Buggy, yes. Check the mailing list, check the code yourself, as you love
to say.
Guillem
Opening file pull1.pdo.gz.
Hi,
Use editconf. You can center the protein and align its main axis ( -princ
) or play around with the rotation of the initial orientation ( -rotate ).
Then get the surface of the correct (aligned and centered) oritentation as
input for making the hole (if you want to use the modified md code).
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