Dear Justin:
I have another question, this time about LJ 1-4 interactions.
I notice that charmm36-jun2015.ff/ffbonded.itp has the following in [ pairtypes
]
NH1 S 1 0.316269044940 1.2552
and it has the following in [ atomtypes ]
S1632.060.000 A
Hi All,
Just an update. I regenerated the topology for the linear peptide with the
ATB and found myself with similar problems.
Will this pull until the Z-component of the COM distance is 3.2 nm and hold
it in place?
pull= yes
pull_ngroups= 2
pull_ncoords
Justin found my error. Energies in gmx and charmm now match.
Here was Justin's fix to my charmm input script to get the full non-periodic
unshifted energies from charmm:
update cutnb 999.0 ctofnb 998.0 ctonnb 997.0 switch vswitch
ener
Thank you Justin!
Thank you very much Justin. I appreciate your time, especially since I expect
that I'm simply not doing what I think I am doing with the charmm test.
I have provided a 15 MB tarball here:
https://www.dropbox.com/s/6hxgc10m9q2p1ze/forJustin.tgz?dl=1
One thing I just noticed is that if I change
In Gromacs/4.6, I used init to define the distance from the solvent COM
that the solute should be pulled to. Has it changed for Gromacs/5.1?
What should I do if I want to pull the solute to [0, 1, 2, 3] nm away from
the solvent COM?
Here is the section I think you are talking about also:
Pull
On 8/7/16 1:13 PM, Dan Gil wrote:
Hi,
I've made the change you suggested. The output file pullx.xvg has changed
from something like:
@ s0 legend "1"
@ s1 legend "1 dZ"
0. 3.01072 3.01072
0.2000 2.98101 2.98101
0.4000 2.94186 2.94186
0.6000 2.95316 2.95316
to this:
@ s0 legend "1"
@ s1
Hi,
I've made the change you suggested. The output file pullx.xvg has changed
from something like:
@ s0 legend "1"
@ s1 legend "1 dZ"
0. 3.01072 3.01072
0.2000 2.98101 2.98101
0.4000 2.94186 2.94186
0.6000 2.95316 2.95316
to this:
@ s0 legend "1"
@ s1 legend "1 dZ"
0. 3.01072 -3.01072
On 8/7/16 11:35 AM, Dan Gil wrote:
Hi,
The pullx.xvg file is returning the coordinates of the solvent, and not the
solute (a_Cooh) as I want.
The solute is being pulled in a coordinate other than Z, although I specify:
pull-coord1-dim =N N Y
What is going on here?
Swap
pull-coord1-groups
Hi,
The pullx.xvg file is returning the coordinates of the solvent, and not the
solute (a_Cooh) as I want.
The solute is being pulled in a coordinate other than Z, although I specify:
pull-coord1-dim =N N Y
What is going on here?
On Sun, Aug 7, 2016 at 7:20 AM, Billy Williams-Noonan <
On 8/7/16 2:21 AM, Christopher Neale wrote:
Dear Gromacs users:
This is a hybrid gromacs/charmm question, but there is not such a mailing
list and I am hoping this is a suitable place for this question.
You can send these questions directly to me; I maintain the port and did a lot
of the
Hi All,
I'm having a similar problem and wouldn't mind some advice either. I am
getting LINCS warnings on one cluster that I run my sampling on, but the
pull-code works fine on other clusters we have access to, which is making
me doubt the entire process.
Best regards,
Billy
On 7 August 2016
ing 3QRH_C.err
<https://cgenff.paramchem.org/initguess/#20160807/3QRH_C.err> Now processing
molecule /scrat ...attype warning: carbon radical, carbocation or carbanion not
supported;skipped molecule. .."
cold you tell me How I can produce topology of my ligand with this server.
I dont know
Dear Gromacs users:
This is a hybrid gromacs/charmm question, but there is not such a mailing list
and I am hoping this is a suitable place for this question.
I am trying to convert some charmm36 parameters (from a new paper) to gromacs
format and for this I am doing single-point energy
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