Thank you Professor Shirts.
So now my protein itp file looks like this:
[ atoms ]
; nrtype resnr residue atom cgnr chargemasstypeB
chargeB MassB
1 CT1ACECH3 1 -0.190264 12.01 CT_per
-0.12033412.01
[ bonds ]
;ai aj func th0 kb th0
Hi,
Could you please clarify if the hbond existed in frames for which g_sdangle
reported a ADH-angle above 30 deg?
Also, bear in mind that the -merge flag is on by default, so another hydrogen
may bridge the donor-acceptor gap.
Erik
On 24 Apr 2013, at 21:09, kim2811 wrote:
> Hi, is there an
Hi, is there any other criteria in determining a hydrogen bond? i know that
in order for a bond to exist, donor-acceptor distance should be less than
or equal 3.5A and A-D-H angle less than or equal 30deg. I used g_sgangle to
measure the angle A-D-H of two hydrogen bonds identified when I determine
Dear Users:
I am having trouble getting any speedup by using more than one node,
where each node has 2 8-core cpus and 3 GPUs. I am using gromacs 4.6.1.
I saw this post, indicating that the .log file output about number of gpus used
might not be accurate:
http://lists.gromacs.org/pipermail/gmx-
Don't be sorry. It's okay. It's just cultural differences.
2013/4/24 bharat gupta
> I think it should be me who should be sorry. I should have asked the
> question again in the forum without referring to some particular
> individual.
>
>
> On Wed, Apr 24, 2013 at 9:30 PM, massimo sandal >wrote
Dear All,
I am starting to use amber03 force field, but I have found something very
strange for proper angle dihedral.
On the basis of definition of proper dihedral function in AMBER and GROMACS
manual I aspect that the following conversion from amber to gromacs:
k_n(GROMACS)=4.18/2 V_n (AMBER)
Dear All,
I am starting to use amber03 force field, but I have found something very
strange for proper angle dihedral.
On the basis of definition of proper dihedral function in AMBER and GROMACS
manual I aspect that the following conversion from amber to gromacs:
k_n(GROMACS)=4.18/k V_n (AMBER)
Dear All,
I am starting to use amber03 force field, but I have found something very
strange for proper angle dihedral.
On the basis of definition of proper dihedral function in AMBER and GROMACS
manual I aspect that the following conversion from amber to gromacs:
k_n(GROMACS)=4.18/k V_n (AMBER)
I think it should be me who should be sorry. I should have asked the
question again in the forum without referring to some particular
individual.
On Wed, Apr 24, 2013 at 9:30 PM, massimo sandal wrote:
> 2013/4/24 Justin Lemkul
>
> >
> >
> > I haven't said anything because I agree with what Mass
2013/4/24 Justin Lemkul
>
>
> I haven't said anything because I agree with what Massimo has already told
> you. If that is comforting in some way to know, then so be it, but I think
> it is rather rude to suggest that you would rather someone else answer your
> question, even after being given t
On 4/24/13 3:26 AM, James Starlight wrote:
The only possible way to view representation of the configuration volume
of the ligand was the representation of all frames of the ligand along the
trajectory. By the way its not quite understand for me in one case the
measurement of the diffusion c
On 4/24/13 4:49 AM, Giuseppe wrote:
Dear Justin,
there were for sure some errors in the command, but even having solved them,
the protein still move during the optimization. What I noticed is that the
coordinates of the residues seems to decrease to zero and than "restart"
from a point out fro
On 4/24/13 3:06 AM, bipin singh wrote:
Hi all,
Please let me know whether this is the right way to calculate RMSD from the
average structure from a simulation:
g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg
average.pdb: is the pdb file produced using -ox option of g_rmsf.
You can calcu
On 4/23/13 9:43 PM, bharat gupta wrote:
Dear Justin/Mark,
I have asked this question previously in the forum, I got some reply from
other members. It will be more useful if you can provide you expert
comments on the same. I am planning to run REMD for a peptide (406 atoms )+
solvent system (27
Dear gmx/plumed developers,
I know that this is probably a question for the PLUMED mailing list more
than the GMX mailing list but considering that the question involves GROMACS
as well I thought to post it here first.
I have read with great attention the paper by Limongelli et al. published on
t
Dear Justin,
there were for sure some errors in the command, but even having solved them,
the protein still move during the optimization. What I noticed is that the
coordinates of the residues seems to decrease to zero and than "restart"
from a point out from the box. I mean, taking the first atom
The only possible way to view representation of the configuration volume
of the ligand was the representation of all frames of the ligand along the
trajectory. By the way its not quite understand for me in one case the
measurement of the diffusion coefficient could be better than MSD which is
th
Hi all,
Please let me know whether this is the right way to calculate RMSD from the
average structure from a simulation:
g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg
average.pdb: is the pdb file produced using -ox option of g_rmsf.
--
*---
Thanks and Regards,
Bipin Sin
18 matches
Mail list logo
