Dear All,
I'm trying to keep distance restraints between few atoms, and for that I
have done the following,
In the topology file, I have inserted a block specifying the details of
pairs
--
; Include forcefield
Hi Justin,
Thank you very much!
On Thu, Mar 12, 2015 at 9:53 AM, mah maz mahma...@gmail.com wrote:
Dear all,
I have a question probably not related to this mailing list! I want to see
a film of an output trajectory via VMD. I tried the .trr file by the
appropriate format in VMD, it shows
Dear All,
I am simulating a polystyrene melt with OPLS-AA force field. At the moment I
am trying to cut off the bonds connecting styrene units on the chain backbone.
Consequently, all the bond angles and dihedrals crossing these removed backbone
bonds are also deleteted from the *.top file.
On 3/17/15 6:48 AM, Ming Tang wrote:
Moring Justin,
Many thanks to you.
Sorry for the confused expression and the late reply. Today, I run the
simulation step by step following the tutorial again. It turned out that the
code you gave me recovers the behavior of the SMD portion of the
On 3/17/15 8:16 AM, rahul dhakne wrote:
Dear all,
I am trying to perform the Normal Mode Analysis protein in water.
Here is the .mdp file I am using:
integrator = nm; time step
nsteps = 10 ; number of steps
nstlist
Dear gromacs users
Previously, I simulated collagen triple helix chains, (GLY-PRO-HYP)n using
Amber99sb-ILDN forcefield. When I processed pdb structures with pdb2gmx, I
only obtained GLY in the N termini properly, and HYP was not processed(it
was treated like HYP, not terminal HYP) since there
Hi,
I am running MD for dsDNA-protein complex. After 50ns I observed that the
DNA is unwinding. What did go wrong? Should I have changed something in my
input file?
Thank you in advance for your suggestions.
best regards
Urszula
-
Ta wiadomość została
On 3/16/15 9:17 AM, Tushar Ranjan Moharana wrote:
Hi Justine,
As you can see in my .itp file the atom number starts from 1. Even this is
the case with index file. I tried to modify index file to have atomic
number same as pdb file but it gave a blank output. So my first concern is
how GROMACS
On 3/17/15 12:12 AM, Thomas Lipscomb wrote:
Dear gmx-users,
I am repeating the KALP15 in DPPC tutorial using Maximin 3 in DPPC using the CHARMM36
forcefield. I think the lipid shrinking was a step I did badly last time (I think I was
getting can open em.tpr but not open em1.tpr, em2.tpr,
Moring Justin,
Many thanks to you.
Sorry for the confused expression and the late reply. Today, I run the
simulation step by step following the tutorial again. It turned out that the
code you gave me recovers the behavior of the SMD portion of the tutorial, and
the problem is the distances.pl
2015-03-17 14:35 GMT-03:00 Urszula Uciechowska
urszula.uciechow...@biotech.ug.edu.pl:
Hi,
I am running MD for dsDNA-protein complex. After 50ns I observed that the
DNA is unwinding. What did go wrong? Should I have changed something in my
input file?
You might want to send your input
Hi, Leandro
Thanks for your explanation and tips. It helped me a lot.
Initially, I'll try to do the parameterization for the fluorophore and
substrate using GAFF and Antechamber, and then combine it with the AMBER
forcefield. After that, I'll apply this new forcefield to carry out the MD
Dear users,
I tried to remove the jumps of a structure after simulation but I couldn't
do it. The structure is heterodimer. I tried the following ways:
1)
-gmx trjconv -f md.xtc -s md.tpr -o traj_nojump.xtc -pbc nojump
-gmx trjconv -f traj_nojump.xtc -s md.tpr -o traj_center.xtc -pbc mol -ur
Hi Justin,
Thanks a lot. I can move forward now.
Recently, I am trying to pull a triple helix, and want to fix the center of
mass of the three terminal atoms. One paper said that it can be done by means
of a strong harmonic restrain with a super large spring constant in Gromos96 53
a6. But I
Yes, it can not run. But I can extract the COM of different conf.groone by one
manually. Due to the time difference, I will update the error message when I
get to the office.
Thanks.
Sent from my Huawei Mobile
Justin Lemkul jalem...@vt.edu wrote:
On 3/17/15 6:48 AM, Ming Tang wrote:
Moring
Hi Justin,
Here is the error message.
tm@tm-HP-Z420-Workstation:~/umbrella$ perl distances.pl
Bareword found where operator expected at distances.pl line 8, near gmx
distance -n index.ndx -s pull.tpr -f conf${i}.gro -select 'com of group
Chain_A
(Missing operator before Chain_A?)
String
On 3/17/15 8:08 PM, Ming Tang wrote:
Hi Justin,
Here is the error message.
tm@tm-HP-Z420-Workstation:~/umbrella$ perl distances.pl
Bareword found where operator expected at distances.pl line 8, near gmx distance -n
index.ndx -s pull.tpr -f conf${i}.gro -select 'com of group Chain_A
Hi,
Related to the Zn-parameters; where can I find the reference (author,
journal, year) to the sigma and epsilon (1.95998e-01 5.23000e-02)
parameters that I find in /gromacs/top/amber99sb.ff/ffnonbonded.itp for
[
atomtypes ] Zn.
I would like to use amber99sb force field in my
Dear Gromacs Users,
I want to show distribution of water inside the peptide based cylindirical
nanofiber. To do this:
1) I created an index file which contains OW atoms (=Oxygen atoms belongs
to the water molecules)
2) Then, I used the following command:
g_rdf -f traj.xtc -s OW.ndx -o
Dear all,
I am trying to perform the Normal Mode Analysis protein in water.
Here is the .mdp file I am using:
integrator = nm; time step
nsteps = 10 ; number of steps
nstlist = 10; update
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