Pablo Englebienne wrote:
Thanks for the suggestions, Justin.
I'm still having issues with instabilities and large fluctuations in
unconstrained NPT simulations of the CHCl3 box, so I'll appreciate
comments from the list on my run parameters. I think there is a problem
with the pressure coup
Thanks for the suggestions, Justin.
I'm still having issues with instabilities and large fluctuations in
unconstrained NPT simulations of the CHCl3 box, so I'll appreciate
comments from the list on my run parameters. I think there is a problem
with the pressure coupling, but I'm not sure what
Pablo Englebienne wrote:
Following up on the previous message, I noticed that the topology I
previously sent (including 10 bonds) works for a minimization, but not
for an MD simulation. grompp issues the following warning:
WARNING 1 [file topol.top, line 29]:
Molecule type 'CHCL3' has 10 co
Following up on the previous message, I noticed that the topology I
previously sent (including 10 bonds) works for a minimization, but not
for an MD simulation. grompp issues the following warning:
WARNING 1 [file topol.top, line 29]:
Molecule type 'CHCL3' has 10 constraints.
For stability an
Pablo Englebienne wrote:
OK, I started over with the CHCl3 box from scratch. I prepared the
following itp file from the CHCL3 parameters in ffG53a5.rtp:
---[chcl3.itp]---
[ moleculetype ]
; Namenrexcl
CHCL3 3
[ atoms ]
; nr type resnr residue atom cgnr
OK, I started over with the CHCl3 box from scratch. I prepared the following
itp file from the CHCL3 parameters in ffG53a5.rtp:
---[chcl3.itp]---
[ moleculetype ]
; Namenrexcl
CHCL3 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1
Pablo Englebienne wrote:
Thanks for confirming this, Justin.
I decided not to use the user-contributed CHCl3 box because the topology
is not consistent with the GROMOS atom types: the CH is united atom
(although the mass is 12.01100, it should probably be 13.01900?), while
in G53a5 there a
I'm trying to simulate a small molecule in a chloroform box using the
GROMOS G53a5 forcefield. I realized that the parameters for the
solvent
are present in the ffG53a5.rtp file, however I could not find a CHCl3
solvent box included in GROMACS. I did find, however, a CHCl3 solvent
box equilib
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