look for either -dt or -skip.
Dr. Vitaly V. Chaban
On Mon, Jul 15, 2013 at 2:03 AM, Rama ramkishn...@gmail.com wrote:
Hi,
How to get a snapshots in equal intervals of time (250ps) from production
MD
trajectory. I'm using -sep , -t0, -timestep but output came only one .gro
file.
--
Hi
I want calculate the enthalpy of water molecule corresponding to protein
folded and unfolded state.
How much a single water molecule (enthalpy and free energy) contribute in
folding ?
Can we calculate enthapy from g_energy?
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Sure, you can.
Dr. Vitaly V. Chaban
On Mon, Jul 15, 2013 at 8:38 AM, pooja_gu...@nccs.res.in wrote:
Hi
I want calculate the enthalpy of water molecule corresponding to protein
folded and unfolded state.
How much a single water molecule (enthalpy and free energy) contribute in
folding ?
On 07/15/2013 10:20 AM, Dr. Vitaly Chaban wrote:
Sure, you can.
Dr. Vitaly V. Chaban
I've got a question for it. Why the calculated entropy is negative?
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Thanks Vitaly
but how??
let's say the difference between unfolded to folded protein is 100 water
molecules. What is the correct procedure to calculate (theoretically) the
entrapy correspond to single water molecule for stabilizing/destabilizing
the protein.
help me
Sure, you can.
Dr.
H = U +pV, all these terms are available through g_energy.
Your resulting values will be per mole, so I would perform no additional
normalization.
Personally, I would simulate all cases (folded, unfolded, etc) with the
same number of waters -- to avoid any possible artifacts.
Dr. Vitaly V.
Hello,
I'm trying to simulate liquid water (512 water molecules) with SMW4-NPD
polarizable force field. The NVT simulation looks fine, but when I restart it
with NVE runs, the total energy of the system keeps drifting down.
The time step I'm using now is 0.5 fs and emtol=0.01 kJ/mol/nm.
Dear Justin
I don't know how can I detect the protonation state of amino acids in specific
pH. Can you help me?
Thank you
Fatemeh Ramezani
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On 7/15/13 7:56 AM, fatemeh ramezani wrote:
Dear Justin
I don't know how can I detect the protonation state of amino acids in specific
pH. Can you help me?
There are various methods for pKa calculations, and based on those results you
can choose the appropriate states with pdb2gmx
Hi,
I have a 20 ns long trajectory which has become corrupted beyond 18ns. I
have the full checkpoint file. Is there any way I can use mdrun and the .cpt
to rerun the simulation from 18ns and append it to the current .xtc (After I
have clipped the part beyond 18ns by trjconv)? I did not find the
On 7/15/13 8:38 AM, Rajat Desikan wrote:
Hi,
I have a 20 ns long trajectory which has become corrupted beyond 18ns. I
have the full checkpoint file. Is there any way I can use mdrun and the .cpt
to rerun the simulation from 18ns and append it to the current .xtc (After I
have clipped the part
Hi Justin,
The checkpoint file has gone on to 20 ns. If I do a rerun, the simulation
will finish in one step.
On Mon, Jul 15, 2013 at 6:11 PM, Justin Lemkul jalem...@vt.edu wrote:
On 7/15/13 8:38 AM, Rajat Desikan wrote:
Hi,
I have a 20 ns long trajectory which has become corrupted beyond
Dear Justin
I usepropka site for pKa calculation but I want to know if pKa is smaller than
my desired pH , I must consider this amino acid deprotonate?
and if pKa of aminoacids is bigger thanmy desired pH, I must protonate this
amino acid?
Thank you
Fatemeh Ramezani
-
I guess, the more important question is whether the checkpoint file stores
the previous checkpoints as well. If it stores only the last checkpoint at
20 ns, then I guess there is no way to rerun from 18 ns.
I do not store a .trr because of space constraints and hence I do not have
the velocities.
On 7/15/13 8:52 AM, rajat desikan wrote:
Hi Justin,
The checkpoint file has gone on to 20 ns. If I do a rerun, the simulation
will finish in one step.
You need a checkpoint file that corresponds to a good frame before the
corruption. If you don't have that, you can't fix the broken
On 7/15/13 8:54 AM, fatemeh ramezani wrote:
Dear Justin
I usepropka site for pKa calculation but I want to know if pKa is smaller than
my desired pH , I must consider this amino acid deprotonate?
and if pKa of aminoacids is bigger thanmy desired pH, I must protonate this
amino acid?
On 7/15/13 8:56 AM, rajat desikan wrote:
I guess, the more important question is whether the checkpoint file stores
the previous checkpoints as well. If it stores only the last checkpoint at
20 ns, then I guess there is no way to rerun from 18 ns.
It does not. Checkpoints are recycled
Thank you!
On Mon, Jul 15, 2013 at 6:29 PM, Justin Lemkul jalem...@vt.edu wrote:
On 7/15/13 8:56 AM, rajat desikan wrote:
I guess, the more important question is whether the checkpoint file stores
the previous checkpoints as well. If it stores only the last checkpoint at
20 ns, then I
Hi,
The following command I used for the snapshots but I'm getting one frame
time 0 time 500. what are the changes I need to do in the command to get
snapshots in equal intervals of time for ex: 250ps. My production MD
trajectory was 15ns.
g_trjconv -s md.tpr -f md.trr -o beta.gro -skip 1 -dt 0
On 7/15/13 9:02 AM, Rama Krishna Koppisetti wrote:
Hi,
The following command I used for the snapshots but I'm getting one frame
time 0 time 500. what are the changes I need to do in the command to get
snapshots in equal intervals of time for ex: 250ps. My production MD
trajectory was 15ns.
Thank you very much *Justin*.
--
Rama
On Mon, Jul 15, 2013 at 8:06 AM, Justin Lemkul jalem...@vt.edu wrote:
On 7/15/13 9:02 AM, Rama Krishna Koppisetti wrote:
Hi,
The following command I used for the snapshots but I'm getting one frame
time 0 time 500. what are the changes I need to
On 7/15/13 9:11 AM, fatemeh ramezani wrote:
Dear Justin
I know the Henderson-Hasselbalch equation, but what should I consider [A-]/[HA]
for amino acids?
That's what you're solving for. You know pH and pKa, and that tells you the
ratio of deprotonated to protonated species, which tells
Hi,
the following:
trjconv -s md.tpr -f md.trr -o beta.gro -dt 250 -sep
should work.
-dt 250 ; write output every 250 ps
-sep ; to write each frame (but the output frequency gets overwritten by
'-dt 250')
the additional use of '-dump x' might be the problem, since with '-dump
x' GMX writes
Thanks *Thomas*
--Rama
On Mon, Jul 15, 2013 at 9:00 AM, Thomas Schlesier schl...@uni-mainz.dewrote:
Hi,
the following:
trjconv -s md.tpr -f md.trr -o beta.gro -dt 250 -sep
should work.
-dt 250 ; write output every 250 ps
-sep ; to write each frame (but the output frequency gets
Justin Lemkul wrote
The .cpt file stores information related to output frequency. The
existing.cpt
file designates output every X steps, while the new .tpr file specifies
output
every Y steps, and X != Y, so mdrun complains. I'm assuming mdrun aborts
at
that point? Have you tried with
On 7/15/13 11:48 AM, Neha wrote:
Justin Lemkul wrote
The .cpt file stores information related to output frequency. The
existing.cpt
file designates output every X steps, while the new .tpr file specifies
output
every Y steps, and X != Y, so mdrun complains. I'm assuming mdrun aborts
at
that
Hi,
I saved my coordinates every 500ps in production MD run, could I alter now
.xtc file by saving different coordinates for ex: every 100ps. Is there any
command to alter the files.
Thanks in Advance
--Rama
--
View this message in context:
On 7/15/13 12:08 PM, Rama wrote:
Hi,
I saved my coordinates every 500ps in production MD run, could I alter now
.xtc file by saving different coordinates for ex: every 100ps. Is there any
command to alter the files.
You can't create frames that aren't there. You can decrease the frame
O
kay...
T
hanks for prompt reply *Justin*
*
.
--Rama
**
*
On Mon, Jul 15, 2013 at 11:11 AM, Justin Lemkul jalem...@vt.edu wrote:
On 7/15/13 12:08 PM, Rama wrote:
Hi,
I saved my coordinates every 500ps in production MD run, could I alter now
.xtc file by saving different coordinates
Whats the energy of each waters hydrogen bonding strength respective of each one...as they vary by a couple kcal/mol according to the new IUPAC standard deffinition of hydrogen bonds (2011)? And the energy of the internal structural hydrogen bonds that were disrupted? Assuming no acidic
On Mon, Jul 15, 2013 at 3:00 AM, gmx-users-requ...@gromacs.org wrote:
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Hi Gromaxers,
Thanks for previous answers.
I have to simulate reverse micelle after solvation with isooctane.My system now
is:
ISOOCTANE(solvent)+AOT(surfactant)+coreWATER.
When I do grompp, it says moleculetype SOL is redefined and
Dear users,
How do I get the force-field for ClO4- ion in the gromacs?
Thanks in advance.
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