First check your .gro file and your .top file, to make sure atom 6518 (or
Water) is consistently defined.
Next step would be to make sure this atom features in the index file within a
"correct group".
In some cases, if a single atom is left out and not part of any group in the
index file, it gives
Justin,
thanks again for explanation.
I've tried examine that parameters more carefully. E.g in my system
with 2 atom types I defined in topology
[ atomtypes ]
;name at.num mass charge ptype c6 c12
CH26 0.000 0.000 A 0.0023406244 4.937284e-06 ; CB
Thank Neha ! I follow your advices but this error still appear. I don't
know why.
By the way, does anybody know why there are not ions in topology file in
Martini CG-MD. Because I see the system has not zero charge, i don't
understand why the CG system not be neutralized by ions.
Thanks and regar
Dear users,
I'm simulating a system of protein/water/popc/ions. The peptide is inserted
through the transmembrane, and the peptide acts as a channel.
In order to reduce the trajectory storage volume, I need to use xtc-grps in
.mdp file. In my system, I'd rather to store the positions of peptide,
On 1/4/13 12:51 AM, Kieu Thu Nguyen wrote:
Dear All,
When using the command
grompp -f equi.mdp -c membedded.gro -p merged.top -n index.ndx -o
equilibrate.tpr
The error is
Fatal error:
Invalid atom number 6518 in indexfile
How can i fix this ?
Hard to say. You haven't told us what's in the s
On 1/4/13 5:06 AM, Kieu Thu Nguyen wrote:
Thank Neha ! I follow your advices but this error still appear. I don't
know why.
You'll have to show us exactly what you're doing to get any solid advice.
Consider what I posted earlier. Usually the mismatch occurs because you are
using a coordin
On 1/4/13 5:01 AM, James Starlight wrote:
Justin,
thanks again for explanation.
I've tried examine that parameters more carefully. E.g in my system
with 2 atom types I defined in topology
[ atomtypes ]
;name at.num mass charge ptype c6 c12
CH26 0.000
On 1/4/13 9:16 AM, Steven Neumann wrote:
Dear All,
What are the units used in Charmm ff in Gromacs for nonbonded parameters?
Is that kJ/mol for Epsilon or kcal/mol ?
Is that A or nm for sigma?
See the manual, chapter 2. Particularly Tables 2.1 and 2.2.
-Justin
--
On 1/4/13 11:09 AM, Shima Arasteh wrote:
Dear users,
I'm simulating a system of protein/water/popc/ions. The peptide is inserted
through the transmembrane, and the peptide acts as a channel.
In order to reduce the trajectory storage volume, I need to use xtc-grps in .mdp file. In
my system,
Justin, thanks for explanation again!
So if I understood correctly in the ffnonbonded c6 correspond to the
attraction term and c12 to the repulsion term doestn't it ? So might
the vdw radius of the atom be increased/ deacreased via corrections in
the c6 term ?
mass charge ptype
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