2016-08-30 13:18 GMT-06:00 Chang Woon Jang :
> Dear Christoph,
>
> I think that bond potentials seem to be good with U shape using
> csg_call --options options.xml --ia-type bond --ia-name bond
> convert_potential gromacs
Yeah, the attached bond potentials actually
Dear Christoph,
I think that bond potentials seem to be good with U shape using
csg_call --options options.xml --ia-type bond --ia-name bond
convert_potential gromacs
The following potentials in figures are obtained from csg_call. I am
not sure of forces though. With all those
2016-08-30 12:33 GMT-06:00 Chang Woon Jang :
> Dear Christoph,
>
>It runs smoothly up to 12500 iterations. After that the error still exist
> as follows. Luckily, 10K iterations do not produce the error.
The below error means a bond got stretched more than 2.02391 nm,
2016-08-30 12:22 GMT-06:00 Chang Woon Jang :
> Dear Christoph,
>
>Did you also change original bond and angle tables to gromacs format?
I only looked at the dihedral!
>
> If so, how do I determine the min and max values for bond and angle tables?
Basically you look at
Dear Christoph,
It runs smoothly up to 12500 iterations. After that the error still
exist as follows. Luckily, 10K iterations do not produce the error.
DD step 12499 load imb.: force 5.6%
Step Time Lambda
125006.250000.0
Hi,
thanks for sending the potentials.
Here is what I did:
$ ls table_d*.txt
table_d1.txt table_d2.txt table_d3.txt table_d4.txt
# These are the potentials out of csg_boltzmann
$ cat table_d.xml
dihedral
-3.141
3.141
0.001
1e8
0.001
$
2016-08-29 15:19 GMT-06:00 Chang Woon Jang :
> Dear Christoph,
>
>Can I run ibi without dihedrals? Actually, I do not need dihedral
> potentials even though CG molecules have dihedrals. Or, any suggestions for
> debugging the dihedrals. Actually, the warning signs
Dear Christoph,
Can I run ibi without dihedrals? Actually, I do not need dihedral
potentials even though CG molecules have dihedrals. Or, any suggestions for
debugging the dihedrals. Actually, the warning signs disappeared but I have
still the same Fatal error.
Thank you.
Best regards,
2016-08-29 13:32 GMT-06:00 Chang Woon Jang :
> Dear Votca Users,
>
>I have four dihedral distributions directly from csg_boltzmann. However,
> only one dihedral distribution gives waning sign during IBI run as follows.
>
> WARNING: For the 359 non-zero entries for
Dear Votca Users,
I have four dihedral distributions directly from csg_boltzmann. However,
only one dihedral distribution gives waning sign during IBI run as follows.
WARNING: For the 359 non-zero entries for table 0 in table_d1.xvg the
forces deviate on average 196% from minus the numerical
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