Hi Mark,
Your analyses are
quite reasonable. The low-temperature replicas are indeed doing much more work
than the high-temperature replicas. As you said, the lowest temperature replica
in the 24-replica should take an amount of time comparable to that of the
lowest in the 42-replica. So for
Hello,
Is there a way to continue minimizing after reaching machine precision? Emtol
and the number of iterations are sufficient to continue.
I am assuming that reaching machine precision means that the gradient of change
from one iteration to another has become so small that further
Hello,
Is there a way to continue minimizing after reaching machine
precision? Emtol and the number of iterations are sufficient to continue.
I am assuming that reaching machine precision means that the gradient
of change from one iteration to another has become so small that
further
Hi all,
I am getting following during while running
pdb2gmx for a RNA moleculei am using amber99sb force field parameters
The details of the error is as:
Fatal error:
In the chosen force field there is no residue type for 'ARG' as a starting
terminus
For more information and tips for
Hi all,
Hi
I've converted the OPLS-AA torsional potential parameters for the
alkane C-C-C-C (CT-CT-CT-CT in the gromacs parameter file notation),
C-C-C-H (CT-CT-CT-HC), and H-C-C-H (HC-CT-CT-HC) torsions from the
OPLS format given in Jorgensen et al, JACS 118, 11225 (1996)
to the
Hi,guys
I obtained surface tension of water and salt solution. But the value RMSD was
always very big although the value of 65 is reasonable. Is it all right about
the RMSD??
Energy Average Err.Est. RMSD Tot-Drift
Hi,guys
I obtained surface tension of water and salt solution. But the value RMSD was
always very big although the value of 65 is reasonable. Is it all right about
the RMSD??
Energy Average Err.Est. RMSD Tot-Drift
There is no error. The alkane dihedral parameters were updated in 1999, and
differ from those originally published in 1996.
Andrew
On Tue, Feb 8, 2011 at 5:20 AM, sulatha M. S mssula...@gmail.com wrote:
Hi all,
Hi
I've converted the OPLS-AA torsional potential parameters for the
alkane
Dear all
I would like to do coarse-grained simulations using reduced LJ units. As I
can see in the manual, this is possible, but I don't understand how...
I use the Gromos96 53a6 force field.
In the *ffG53a6nb.itp *the* σ* and *ε* are in *(nm*) and *(KJ/mol*)
Also in the *ffG53a6.atp* the
hello
Now it is almost clear what happened. When couple-intramol is no (default),
all pairwise vdm and charge interaction becomes bonded interaction.
All intra-molecular non-bonded interactions for moleculetype couple-moltype
are replaced by exclusions and explicit pair interactions. In this
This was very useful for me
http://www.sunsetstripbillboards.com/info.html Wanna share with you.
--
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I am a humanist, which means, in part, that I have tried to behave decently
without expectations of rewards or punishments after I am dead.
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Dear All,
I have performed a simulation of POPC with polarisable water model in
presence of 0.2 mol CaCl2 based on MARTINI CG model. I used shift for the
electrostatic interactions and the job was done on a 8-core node with
domain decomposition 2 2 2. The lipid bilayer consists of 512 lipid and
Dear gmxusers,
I need to perform molecular dynamics simulation of a B2AR within the
POPC membrane. I have downloaded the 128b.pdb, popc.itp and lipid.itp
files from Prof.Tieleman's group. My protein of interest is 343
residues. Also, I aligned the protein and membrane. I followed the
Justin
Aldo Segura wrote:
Dear gmxusers,
I need to perform molecular dynamics simulation of a B2AR within the
POPC membrane. I have downloaded the 128b.pdb, popc.itp and lipid.itp
files from Prof.Tieleman's group. My protein of interest is 343
residues. Also, I aligned the protein and membrane. I
Thanks for your answer. You're right in the procedure for the packing
of the protein and lipids. However, after several iterations (~30) the
lipids are packaged to form the bilayer and the protein is outside of
it. I can send you a couple of pictures for a better explanation of my
problem.
Aldo Segura wrote:
Thanks for your answer. You're right in the procedure for the packing
of the protein and lipids. However, after several iterations (~30) the
lipids are packaged to form the bilayer and the protein is outside of
it. I can send you a couple of pictures for a better explanation
Dear Justin,
You're right, I corrected the box vectors , and it works!
Thanks,
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Please don't
Hi,
I want to calculate the RMSF of residues and not of protein ... how can this
be done with g_rmsf..
Also I want to see the rmsf of certain residues .. for which I created the
.ndx file containint those residues only .. and after using g_rmsf with
index file gives the RMSF for whole protein
bharat gupta wrote:
Hi,
I want to calculate the RMSF of residues and not of protein ... how can
this be done with g_rmsf..
Also I want to see the rmsf of certain residues .. for which I created
the .ndx file containint those residues only .. and after using g_rmsf
with index file gives
Actually after loop incorporation I want to check which region of the
protein shows much deviation , which I think can be done by plotting rmsf
values from both proteins.. but the problem here is that one structure which
contains loops has more no. of atoms as compared to other str. without loop
bharat gupta wrote:
Actually after loop incorporation I want to check which region of the
protein shows much deviation , which I think can be done by plotting
rmsf values from both proteins.. but the problem here is that one
structure which contains loops has more no. of atoms as compared to
try -res option
On Wed, Feb 9, 2011 at 08:51, Justin A. Lemkul jalem...@vt.edu wrote:
bharat gupta wrote:
Actually after loop incorporation I want to check which region of the
protein shows much deviation , which I think can be done by plotting rmsf
values from both proteins.. but the
Hi Justin
Thanks a lot.
I tried doing energy minimization and th lowering emtotal to 200 and
the system converged to
Steepest Descents converged to Fmax 200 in 1411 steps
Potential Energy = -3.9063050e+05
Maximum force = 1.3442458e+02 on atom 927
Norm of force = 1.4758101e+01
For
I used the -res option ... and I got the rmsf in terms of residues but still
the problem is that the two structures contain different amount of residues
due to loop replacement in one structure.. In that case how shall proceed to
check the effect of loop insertion on the overall topology of the
Hi Bharat,
You can do it with post-processing the data you obtain from g_rmfs, if
it's okay that the fit uses all residues in either case. Otherwise,
you can make an two index files, including only the residues that are
common to both.
Hope it helps,
Tsjerk
On Wed, Feb 9, 2011 at 5:58 AM,
You calculate rmsf of both proteins separately and then plot them together
and look the region of your interest..
On Wed, Feb 9, 2011 at 10:28, bharat gupta bharat.85.m...@gmail.com wrote:
I used the -res option ... and I got the rmsf in terms of residues but
still the problem is that the
Thanks for the advice and while creating the index file for first 100 common
residues it found that both structures shows different no.of atoms. .. how
is that possible ??
On Tue, Feb 8, 2011 at 9:00 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Bharat,
You can do it with post-processing
We can't know that. We don't have your files (and we don't want them).
Check what you did, and what index groups you have. Write out the
structure for the index group and have a look. We're not a substitute
for your brain here... :p
Cheers,
Tsjerk
On Wed, Feb 9, 2011 at 6:20 AM, bharat gupta
On 8/02/2011 9:27 PM, bipin singh wrote:
Hi all,
I am getting following during while running
pdb2gmx for a RNA moleculei am using amber99sb force field parameters
The details of the error is as:
Fatal error:
In the chosen force field there is no residue type for 'ARG' as a
starting
I looked at the the paper published in 1999, ( Jorgensen et al JACS, 121,
20, 4831, 1999), the aliphatic torsional parameters are the same as those
from 1996. here are the values,
V1
V2V3 (kcal/mol)
CT-CT-CT-CT 1.740
Tsjerk,
Sorry for asking that .. actually I made a silly mistake while selecting
residues.. After plotting the graphs for common regions I found that first
100 amino acids shows a lot of fluctuations (compared to the one without any
loop insertion) ... Does the insertion caused a great change in
Sir,
Actually ARG is present as a ligand bound to RNA molecule
On Wed, Feb 9, 2011 at 11:16, Mark Abraham mark.abra...@anu.edu.au wrote:
On 8/02/2011 9:27 PM, bipin singh wrote:
Hi all,
I am getting following during while running
pdb2gmx for a RNA moleculei am using amber99sb force
On 9/02/2011 4:48 PM, sulatha M. S wrote:
I looked at the the paper published in 1999, ( Jorgensen et al JACS,
121, 20, 4831, 1999), the aliphatic torsional parameters are the same
as those from 1996. here are the values,
V1
V2
On 9/02/2011 4:52 PM, bharat gupta wrote:
Tsjerk,
Sorry for asking that .. actually I made a silly mistake while
selecting residues.. After plotting the graphs for common regions I
found that first 100 amino acids shows a lot of fluctuations (compared
to the one without any loop insertion)
Thanks for your help.
On Wed, Feb 9, 2011 at 11:44, Mark Abraham mark.abra...@anu.edu.au wrote:
On 9/02/2011 4:56 PM, bipin singh wrote:
Sir,
Actually ARG is present as a ligand bound to RNA molecule
Then you've got work to do. pdb2gmx copes well with linear polymers of
Sorry for not giving the manual version earlier. P. 63 of manual 4.0 is what
I am referring to. The equations relate to converting the OPLS torsional
parameters to RB parameters in GROMACS with the OPLS ff.
The equations are
C0 = V0+V2+0.5(V1+V3)
C1= 0.5(3 * V3-V1)
C2= -V2 + 4 * V4
C3= -2 * V3
Hi,
Anyone has successfully tried to add some new force field in the default
force field (in 4.5)
so pdb2gmx can show up the (newly-added) force field which will also be
recognized by gromacs,
Thanks,
lina
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