Dear users,
Although this topic has been extensively discussed
in the list previously, I am unclear about the solution
for the problem..
While running ligand in water simulation (EM) with RF-0
I get the following message:
:52 AM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
When the simulation was carried out with PME
rcoulomb was set equal to rlist. But when I need to
to ligand-water simulation without PME (with RF-0)
then it requires rlist greater by 0.1-0.3 than rcoulomb.
So if I rerun protein-ligand
Thank you..
On Wed, Nov 6, 2013 at 7:39 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/6/13 5:47 AM, Kavyashree M wrote:
Dear users,
Sorry for repeating the same question. I just wanted to know
whether is it ok if I have rlist rcoulomb in ligand-water and
prot-lig-water rerun md
in the energies isnt it?
Thank you
Regards
Kavya
On Sat, Nov 2, 2013 at 9:51 PM, Kavyashree M hmkv...@gmail.com wrote:
Ok thank you. I thought it was for protein-ligand-water
that needs to be rerun without PME.
Thanks
Regards
Kavya
On Sat, Nov 2, 2013 at 9:45 PM, Justin Lemkul jalem
Sir,
Thank you. Should the ligand-water MD be done without PME?
Thank you
Regards
Kavya
On Sat, Nov 2, 2013 at 9:13 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/2/13 1:22 AM, Kavyashree M wrote:
Dear Users,
Its mentioned in the list that it would be
wrong to use g_lie
Ok thank you. I thought it was for protein-ligand-water
that needs to be rerun without PME.
Thanks
Regards
Kavya
On Sat, Nov 2, 2013 at 9:45 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/2/13 12:14 PM, Kavyashree M wrote:
Sir,
Thank you. Should the ligand-water MD be done without PME
Dear Gromacs users,
I have a protein-ligand in water simulation (Gmx 4.5.3), for
calculating free energy of ligand binding, a separate simulation
of ligand in water simulation is required (which I read from the
list). The question is the protein-ligand is simulated as a dimeric
system so is it
Dear Users,
Its mentioned in the list that it would be
wrong to use g_lie on a simulation which
uses PME.
So kindly suggest any other way available
to get the free energy of ligand binding other
using g_lie?
Thank you
Regards
kavya
--
gmx-users mailing listgmx-users@gromacs.org
Dear users,
For some analysis I require the 27 periodic images
of the system I ran the simulation for. Kindly let me
know how can it be written to a pdb file.
Thanking you
Regards
Kavya
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
*
Thank you Sir!
Regards
Kavya
On Fri, Sep 27, 2013 at 12:52 AM, Tsjerk Wassenaar tsje...@gmail.comwrote:
Hi Kavya,
genconf -nbox 3 3 3
Cheers,
Tsjerk
On Thu, Sep 26, 2013 at 6:24 PM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
For some analysis I require the 27 periodic
Dear users,
After EM step while running NVT I gor a warning saying -
Largest charge group radii for Van der Waals: 3.798, 1.293 nm
Largest charge group radii for Coulomb: 7.565, 3.798 nm
The sum of the two largest charge group radii (11.362685) is larger than
rlist (1.40)
But this
Ok Thank you.
Regards
Kavya
On Tue, Aug 6, 2013 at 3:02 PM, Justin Lemkul jalem...@vt.edu wrote:
On 8/6/13 2:35 AM, Kavyashree M wrote:
Dear users,
After EM step while running NVT I gor a warning saying -
Largest charge group radii for Van der Waals: 3.798, 1.293 nm
Largest charge
Sir,
But if something went wrong, then over is rather irrelevant, isn't it?
Yes. I am planning to rerun ifI dont get any solution.
So your simulation started from some previous point and re-ran? I don't
see how this would be possible given what you have been posting.
The overlap was
Dear users,
I ran a simulation for 25ns. First 5ns in 8 core machine
and late part in 64 cores. It ran without any problem. The
trajectories were concatenated, jumps are removed and
rmsd was calculated. But there was sudden jump in the
rmsd curve. Is it wrong to run simulations in different
cores
, Aug 1, 2013 at 8:12 AM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
I ran a simulation for 25ns. First 5ns in 8 core machine
and late part in 64 cores. It ran without any problem. The
trajectories were concatenated, jumps are removed and
rmsd was calculated. But there was sudden
, Aug 1, 2013 at 5:18 PM, Justin Lemkul jalem...@vt.edu wrote:
On 8/1/13 3:42 AM, Kavyashree M wrote:
Dear Sir,
First trajectory - traj1.xtc (0 to 5... ns)
Second trajectory - traj2.xtc (5... to 25ns)
But there is no gap in between.
for concatenating -
$ trjcat -f traj1.xtc traj2.xtc -o
Dear users,
For some unknown reasons checkpoint file are not
being created if -cpo is not mentioned (in 4.5.3). Now
I have a trajectory of ~10ns without a checkpoint file.
I tried the following -
tpbconv option to create a new .tpr file so that I can
start form the point I stopped. But manual
Dear users,
While running a ligand bound MD using AMber03 force field. I got the
following error
after ~ 4.9 ns
The initial cell size (1.247705) is smaller than the cell size limit
(1.586683), change options -dd, -rdd or -rcon, see the log file for details
Initially I ran using 64 nodes (till
, Kavyashree M wrote:
Sir,
That is true, previously you had explained regarding this.
Calculation using g_saltbr
1. For g_saltbr I included the following residues -
ASP, HIS, ARG, LYS, GLU. A trajectory and tpr was generated
which contained only these residues. sb was calculated using
Ok. Still the distance is beyond the mentioned
cut-off. The distance of both OD1 and OD2 of
ASP is more than 4 Ang from NH2 of Arg.
Thank you
Regards
Kavya
On Thu, Apr 4, 2013 at 2:25 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/4/13 4:34 AM, Kavyashree M wrote:
Sir,
Why I mentioned
Dear users,
This is regarding an observation while calculating the
salt bridge (sb) using g_saltbr.
I used g_saltbr and g_hbond (with contact option) with
a cut of of 4Ang, for calculating sb in the whole protein
at a single frame.
I made sure that I considered sb between same set of
residues
, Apr 3, 2013 at 10:25 PM, Justin Lemkul jalem...@vt.edu wrote:
On Wed, Apr 3, 2013 at 12:50 PM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
This is regarding an observation while calculating the
salt bridge (sb) using g_saltbr.
I used g_saltbr and g_hbond (with contact option
Dear users,
Kindly clarify my doubt regarding salt bridge calculation.
Thank you
Regards
Kavya
On Mon, Apr 1, 2013 at 3:48 PM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
For calculating salt bridge in proteins I
am using g_hbond instead of g_saltbr.
In g_hbond I use contact
indices to calculate distances,
if you already have the information about atoms involved in salt
bridge interactions.
On Tue, Apr 2, 2013 at 5:10 PM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
Kindly clarify my doubt regarding salt bridge calculation.
Thank you
Regards
Kavya
to calculate salt bridges between
these two indices -
group 1: ASP_GLU__OD1_OD2_OE1_OE2
group 2: ARG_LYS__NZ_NE_NH1_NH2
Thank you
Kavya
On Tue, Apr 2, 2013 at 10:10 PM, Justin Lemkul jalem...@vt.edu wrote:
On 4/2/13 11:58 AM, Kavyashree M wrote:
Sir,
Thank you very much for your reply. I
interesting.
If I had a given set of known SB then I would have definitely
gone for g_dist.
Thank you very much.
Kavya
On Tue, Apr 2, 2013 at 10:45 PM, Justin Lemkul jalem...@vt.edu wrote:
On Tue, Apr 2, 2013 at 1:09 PM, Kavyashree M hmkv...@gmail.com wrote:
Sir,
This g_hbond will generate
Dear users,
For calculating salt bridge in proteins I
am using g_hbond instead of g_saltbr.
In g_hbond I use contact and mention two
indices consisting of
group 1: ASP_GLU__OD1_OD2_OE1_OE2:
group 2: ARG_LYS__NZ_NE_NH1_NH2:
I use the command:
g_hbond_46 -f traj.xtc -s md.tpr -n index.ndx
function. Kb is the Boltzmann constant, and T is the
temperature corresponding to each simulation.
On Sun, Mar 31, 2013 at 10:35 AM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
Can someone kindly explain how g_sham calculates
the free energy landscape of given two quantities say
Dear users,
Can someone kindly explain how g_sham calculates
the free energy landscape of given two quantities say,
rmsd and radius of gyration.
Any references are welcome.
Thank you
with Regards
Kavya
--
gmx-users mailing listgmx-users@gromacs.org
Dear users,
Sorry for an off-topic question..
What is the distance cut-off considered for
hydrophobic contact in protein?
Some paper states 4-8Ang, while some other
considers only till 5Ang. It is reported that this
is a long range interaction.
Any information clarifying this doubt will be very
Dear Users,
As suggested earlier by Erik I used 4.6 to calculate the hydrogen bonds.
Still the
Total intra-protein hydrogen bonds is not equal (MM +MS +SS) hydrogen bond.
Is there any other solution?
Thank you
Kavya
On Fri, Jan 25, 2013 at 4:11 PM, Kavyashree M hmkv...@gmail.com wrote:
Dear
, 2013, at 4:46 PM, Kavyashree M wrote:
Dear Users,
As suggested earlier by Erik I used 4.6 to calculate the hydrogen bonds.
Still the
Total intra-protein hydrogen bonds is not equal (MM +MS +SS) hydrogen
bond.
Is there any other solution?
Thank you
Kavya
On Fri, Jan 25, 2013 at 4:11 PM
at the same time. With -merge this counts as one if you analyze the
entire protein. If you split your analysis such hbonds will show up in both
e.g. SS and MS, hence TOT MM+SS+MS. It's just another way of counting
hbonds.
Erik
On Mar 22, 2013, at 5:32 PM, Kavyashree M wrote:
Sir,
I tried
-- Forwarded message --
From: Kavyashree M hmkv...@gmail.com
Date: Fri, Mar 8, 2013 at 10:45 PM
Subject: query regarding mk_angndx
To: Discussion list for GROMACS users gmx-users@gromacs.org
Dear users,
I used mkang_ndx to create an index file with dihedral angles.
Input
Dear users,
I used mkang_ndx to create an index file with dihedral angles.
Input was:
mk_angndx -s a.tpr -n angle.ndx -type dihedral
output angle.ndx read like this -
[ Phi=180.0_2_43.93 ]
52018192237353627323031
39595758
Sir,
I used gromacs 4.6. I got the point - index file will tell how many
contacts an
atom has made during the trajectory. Whether it has made a contact with an
atom only in once or all the time, in the whole trajectory, it will be
mentioned.
Am I right?
So from the problem I had, can I say that
Thank you Sir.
On Tue, Mar 5, 2013 at 4:33 PM, Erik Marklund er...@xray.bmc.uu.se wrote:
On Mar 5, 2013, at 10:34 AM, Kavyashree M wrote:
Sir,
I used gromacs 4.6. I got the point - index file will tell how many
contacts an
atom has made during the trajectory. Whether it has made
Dear users,
I used the following tool for finding the contacts
g_hbond_46 -f a.xtc -s a.tpr -contact -n a.ndx -r 0.4 -hbm a.xpm -hbn a.ndx
-num a.xvg
From the index file, the number of contacts of each atom was extracted.
This and the
xvg output was compared with another simulation.
It was found
.
Thank you
kavya
On Mon, Mar 4, 2013 at 10:05 PM, Justin Lemkul jalem...@vt.edu wrote:
On 3/4/13 11:25 AM, Kavyashree M wrote:
Dear users,
I used the following tool for finding the contacts
g_hbond_46 -f a.xtc -s a.tpr -contact -n a.ndx -r 0.4 -hbm a.xpm -hbn
a.ndx
-num a.xvg
From
On Mon, Mar 4, 2013 at 11:10 PM, Justin Lemkul jalem...@vt.edu wrote:
When measuring contacts, you don't measure one group, you measure the
number of contacts that occur between groups A and B, which considers all
atoms in those two groups.
I gave a group of hydrophobic atoms in both cases
not been any swapping of the trajectory while analysing.
Thank you
Kavya
On Tue, Mar 5, 2013 at 1:09 AM, Justin Lemkul jalem...@vt.edu wrote:
On 3/4/13 1:10 PM, Kavyashree M wrote:
On Mon, Mar 4, 2013 at 11:10 PM, Justin Lemkul jalem...@vt.edu wrote:
When measuring contacts, you don't
Dear users,
I just wanted a small clarification whether the order of elements in matrix
(-hbm) corresponds to reverse order of elements in the index file (-hbn)
obtained from g_hbond?
Thank you
Kavya
--
gmx-users mailing listgmx-users@gromacs.org
Dear users,
How can I get the number of interactions of each residue
within a cut off as a function of time. just like g_saltbr writes
with the option -sep.
I tried using g_mdmat but it gives an average contact map.
Thank you
Kavya
--
gmx-users mailing listgmx-users@gromacs.org
Thank you!
On Thu, Feb 14, 2013 at 3:38 PM, Erik Marklund er...@xray.bmc.uu.se wrote:
Perhaps g_hbond -contact will do what you want.
Erik
On Feb 14, 2013, at 10:42 AM, Kavyashree M wrote:
Dear users,
How can I get the number of interactions of each residue
within a cut off
Dear users,
After simulation dimers appear separated, I was
able to do saltbridge calculation on this. This will
be different than doing it on a dimer which are together.
Am I correct?
Please reply..
Thank you
Kavya
On Thu, Feb 7, 2013 at 3:39 PM, Kavyashree M hmkv...@gmail.com wrote:
Dear
or
is this acceptable?
Thank you
Kavya
On Thu, Feb 7, 2013 at 4:54 PM, Justin Lemkul jalem...@vt.edu wrote:
On 2/6/13 11:49 PM, Kavyashree M wrote:
Dear users,
Since I am getting the mean square displacements in terms of
several nm^2. I doubt it is wrong. Could anyone please explain
me the solution
.
If any other information is required Please let me know.
Thank you
Kavya
On Thu, Feb 7, 2013 at 5:28 PM, Justin Lemkul jalem...@vt.edu wrote:
On 2/7/13 6:49 AM, Kavyashree M wrote:
Dear Sir,
Thank you for the reply,
It does not cross the boundary. I made the trajectory
so
On Thu, Feb 7, 2013 at 5:31 PM, Justin Lemkul jalem...@vt.edu wrote:
On 2/7/13 6:42 AM, Kavyashree M wrote:
Dear users,
After simulation dimers appear separated, I was
able to do saltbridge calculation on this. This will
be different than doing it on a dimer which are together.
Am I
Lemkul jalem...@vt.edu wrote:
On 2/7/13 7:08 AM, Kavyashree M wrote:
Dear Sir,
Yes it is the same protein. Initially I had not superposed the
structures in the trajectory. But this time I calculated the msd
on a superposed trajectory (of the same simulation). the simulation
is carried out
Dear users,
I have a very basic question in MSD calculation.
g_msd calculation on a protein dimer (~237 aa each)
trajectory gave a plot of msd, with the values ranging
between 1 to 14nm^2.
But is this a sensible MSD? As the values given in a
paper i was referring was in Ang^2
J. Chem. Theory
Kavya
On Wed, Feb 6, 2013 at 3:35 PM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
I have a very basic question in MSD calculation.
g_msd calculation on a protein dimer (~237 aa each)
trajectory gave a plot of msd, with the values ranging
between 1 to 14nm^2.
But is this a sensible
Thank you Sir!
Kavya
On Thu, Feb 7, 2013 at 11:18 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
trjconv -fit rot+trans
Cheers,
Tsjerk
On Thu, Feb 7, 2013 at 6:19 AM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
Which tool can be used to create a trajectory
of structures
Dear users,
Sorry. It is because the unit of the cutoff distance ]is in nm.
Thank you
kavya
On Fri, Feb 1, 2013 at 1:28 PM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
I used g_mdmap to calculate the C-alpha contact map of
the trajectory. the distance cut off of 8.0 Ang was selected
Dear users,
I used g_mdmap to calculate the C-alpha contact map of
the trajectory. the distance cut off of 8.0 Ang was selected
The protein is a dimer of 237 residues. The output of -no was
like this -
#resratio tot mean natm mean/atm
1 1.000 473 473.0001 473.000
2
Dear users,
While calculating the distance matrix using g_mdmat, with -no option,
it gives an xvg output pertaining the total, mean etc contacts of the
residue
within 1.5Ang in the trajectory.
I calculated the same for a single frame (or pdb file)
#resratio tot mean natm mean/atm
1
this discrepancy form before.
Erik
On Jan 24, 2013, at 3:59 PM, Kavyashree M wrote:
Dear Sir,
This is 4.5.3. I have not tried nomerge. I did not use
nomerge option in any of them, So if it has counted
it (Hbond b/w same donor and acceptor but with
different hydrogen) twice in one calculation
be the same?
The difference is 4-5 Hbonds..
Thank you
Kavya
On Thu, Jan 24, 2013 at 7:30 PM, Erik Marklund er...@xray.bmc.uu.se wrote:
Hi. What version was this? Have you tried with -nomerge?
Erik
On Jan 21, 2013, at 10:55 AM, Kavyashree M wrote:
Dear users,
While calculating hydrogen bonds
Dear users,
I have a little confusion -
The hbmap.xpm file gives the existence of each hydrogen bond.
The file mentions -
c #FF /* None */,
o c #FF /* Present */,
Meaning -
character space in white colour means Hbond not present
character o in red colour means Hbond is present.
In
Thank you for the clarification.
On Fri, Jan 25, 2013 at 12:40 AM, Justin Lemkul jalem...@vt.edu wrote:
On 1/24/13 11:03 AM, Kavyashree M wrote:
Dear users,
I have a little confusion -
The hbmap.xpm file gives the existence of each hydrogen bond.
The file mentions -
c #FF
Dear users,
I used g_saltbr to calculate the salt-bridge interactions using:
g_saltbr -f ../traj.xtc -s ../topol.tpr -t 0.4 -sep
It gave the output for each atom-atom interaction within
the given cut-off.
When I checked the atom type that corresponds to the atom
number output in each file, side
Dear users,
I would like to add that in case of ARG or LYS, the sidechain
nitrogen atoms (NE,NZ,NH1,NH2) are present in the output.
The problem s only with GLU and ASP residues.
I use 4.5.3 version
Thank you
kavya
On Thu, Jan 3, 2013 at 3:28 PM, Kavyashree M hmkv...@gmail.com wrote:
Dear
Sir,
I used OPLS-AA ff. Thank you very mush for your effort.
Its clear now. AS you said It assigns the number of the 1st
atom of the charge group in the output file.
Thank you
kavya
On Thu, Jan 3, 2013 at 5:01 PM, Justin Lemkul jalem...@vt.edu wrote:
On 1/3/13 5:15 AM, Kavyashree M wrote
can see, its functionality is entirely duplicated by g_angle,
so g_dih will probably be removed in 4.6. I suggest you use g_angle for
whatever you are trying to do.
Mark
On Wed, Dec 26, 2012 at 4:31 PM, Justin Lemkul jalem...@vt.edu wrote:
On 12/26/12 12:57 AM, Kavyashree M wrote
of group 1.
Thank you
Kavya
On Wed, Dec 19, 2012 at 10:06 PM, Justin Lemkul jalem...@vt.edu wrote:
On 12/19/12 9:37 AM, Kavyashree M wrote:
Dear users,
While using g_hbond, does it make any difference if I give option
18 and 1 or 1 and 18?
Order does not matter.
I wanted to find
Ok thank you.
kavya
On Wed, Dec 19, 2012 at 10:52 PM, Justin Lemkul jalem...@vt.edu wrote:
On 12/19/12 11:43 AM, Kavyashree M wrote:
Sir,
I thought that the order should not matter but when I used 18 - 1
and 1 - 18 the graph were slightly off.
Group 18 is a set of residues
Dear users,
Am I clear with the question?
Thank you
Kavya
On Wed, Dec 12, 2012 at 1:36 PM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
I was calculating solvent accessible surface area for a trajectory
using g_sas. I used an index file with 3 sets (A, B, C) of mutually
exclusive
Dear users,
Anything wrong in my question?
Kindly give some suggestions.
Thank you
Kavya
On Wed, Dec 12, 2012 at 3:23 PM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
Am I clear with the question?
Thank you
Kavya
On Wed, Dec 12, 2012 at 1:36 PM, Kavyashree M hmkv...@gmail.com
?
Francesco
2012/12/12 Mark Abraham mark.j.abra...@gmail.com
On Wed, Dec 12, 2012 at 9:06 AM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
I was calculating solvent accessible surface area for a trajectory
using g_sas. I used an index file with 3 sets (A, B, C) of mutually
Sir,
Oh! I was using sunset index numbers for both. I am sorry. I will try
that and see. First option as protein and next the subset. Thank you
very much.
Kavya
On Wed, Dec 12, 2012 at 8:16 PM, Justin Lemkul jalem...@vt.edu wrote:
On 12/12/12 9:37 AM, Kavyashree M wrote:
Thank you very
I meant subset :)
On Wed, Dec 12, 2012 at 8:21 PM, Kavyashree M hmkv...@gmail.com wrote:
Sir,
Oh! I was using sunset index numbers for both. I am sorry. I will try
that and see. First option as protein and next the subset. Thank you
very much.
Kavya
On Wed, Dec 12, 2012 at 8:16 PM
you
Kavya
On Thu, Dec 6, 2012 at 3:56 PM, Erik Marklund er...@xray.bmc.uu.se wrote:
5 dec 2012 kl. 17.26 skrev Justin Lemkul:
On 12/5/12 11:21 AM, Kavyashree M wrote:
Sir,
Thank you for your suggestions. I decided the cutoff based on
RMSD convergence. I will calculate
simulation per temperature.
And this happened in two proteins that I had simulated both
are form mesophilic origin.
Thank you
Kavya
On Wed, Dec 5, 2012 at 9:36 PM, Justin Lemkul jalem...@vt.edu wrote:
On 12/5/12 10:56 AM, Kavyashree M wrote:
Dear users,
I have simulated a homodimer (both
Dear users,
One more question is. Is there a way to prove
my point?
Thank you
Kavya
On Wed, Dec 5, 2012 at 9:43 PM, Kavyashree M hmkv...@gmail.com wrote:
Sir,
Thank you for the reply. Total simulated time is 50ns.
first 4ns is left and only 4-50ns were considered for
rmsf calculations. T1
. But Is there any other way
by which I can prove this point?
Thank you
Kavya
On Wed, Dec 5, 2012 at 9:46 PM, Justin Lemkul jalem...@vt.edu wrote:
On 12/5/12 11:13 AM, Kavyashree M wrote:
Sir,
Thank you for the reply. Total simulated time is 50ns.
first 4ns is left and only 4-50ns were
Sir,
Oh! Thanks for good suggestion. Will find a way out.
Kavya
On Wed, Dec 5, 2012 at 9:56 PM, Justin Lemkul jalem...@vt.edu wrote:
On 12/5/12 11:21 AM, Kavyashree M wrote:
Sir,
Thank you for your suggestions. I decided the cutoff based on
RMSD convergence. I will calculate
Dear users,
I have simulated a protein dimer using OPLS-AA in 4.5.3 version.
Analysing simulation showed that one of the monomer is out side
the box.
I tried trjconv pbc -nojump and trjconv -pbc mol
still some fraction of a time one of them goes out. Can anyone
suggest some solution to this.
I
Dear users,
I used -center along with -pbc mol selecting protein for both options
Its fine now both monomers are in the box.
Thanks
kavya
On Sun, Dec 2, 2012 at 1:47 AM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
I have simulated a protein dimer using OPLS-AA in 4.5.3 version
Hi Ananya,
Can you try with rvwd 0.9nm and rcolumb with 1.4nm..?
vdw interaction decreases as 1/r^6, while columbic
interaction decreases as (1/r).. so it would be better if
you consider columbic interaction for longer distance
than vdw interaction..
bye
kavya
On Fri, Nov 16, 2012 at 8:32 PM,
regarding this will be helpful for
the users.
bye
kavya
On Fri, Nov 16, 2012 at 8:52 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/16/12 10:10 AM, Kavyashree M wrote:
Hi Ananya,
Can you try with rvwd 0.9nm and rcolumb with 1.4nm..?
vdw interaction decreases as 1/r^6, while columbic
Hi Ananya,
You can refer this.
http://www.gromacs.org/Documentation/How-tos/Doing_Restarts?highlight=restarting
bye
kavya
On Mon, Nov 12, 2012 at 11:27 AM, ananyachatterjee
ananyachatter...@iiserkol.ac.in wrote:
Hi all,
my simulation has stopped due to power failure, can anyone tell me how
Hi ananya,
You can get the coordinates using trjconv:
trjconv -f file.xtc -s file.tpr -o file.pdb -b initial time in ps
-e final time in ps
this will give you pdb at the time you have mentioned.
For your first question- as far as I know you need to check whether
there is any periodic image
stopped when i was
using the whole trajectory. I tried with -dt 2, still the same problem exists.
Kindly suggest a way out of this situation.
Thank you
With Regards
Kavya
On Thu, Jul 12, 2012 at 6:11 PM, Kavyashree M hmkv...@gmail.com wrote:
Dear Sir,
Thank you It worked :). a very usefull
its not
so.
Thank you
kavya
On Fri, Jul 13, 2012 at 9:22 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 7/13/12 11:50 AM, Kavyashree M wrote:
Dear users,
Its the continuation of the question I asked yesterday, Inorder to reduce
the memory usage during g_saltbr calculations i got
Ok... I will try other options.
Thanks
Kavya
On Fri, Jul 13, 2012 at 10:23 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 7/13/12 12:05 PM, Kavyashree M wrote:
Its 50ns 25000 frames. the xtc file is 695MB. it has 16GB RAM. So will
that be insufficient? I have previously run other analysis
Dear Gromacs users,
I was running the saltbridge calculations for a dimeric
protein simulation using g_saltbr, But its taking very
long time, almost four days still its not completed.
Could anyone has suggestion regarding this issue? I am
using the same system -
Intel(R) Core(TM) i7-2600 CPU @
suggestions?
Thank you
Kavya
On Thu, Jul 12, 2012 at 3:39 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 7/12/12 4:51 AM, Kavyashree M wrote:
Dear Gromacs users,
I was running the saltbridge calculations for a dimeric
protein simulation using g_saltbr, But its taking very
long time, almost four
Thanks :). will check whether it makes it faster.
On Thu, Jul 12, 2012 at 4:27 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 7/12/12 6:38 AM, Kavyashree M wrote:
Dear Sir,
That is true as the number of the frames increased the
memory had almost reached 95% but still it has been in
95
me to go this way.. it
appears quite complicated!
Thank you
Kavya
On Thu, Jul 12, 2012 at 4:52 PM, Kavyashree M hmkv...@gmail.com wrote:
Thanks :). will check whether it makes it faster.
On Thu, Jul 12, 2012 at 4:27 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 7/12/12 6:38 AM, Kavyashree M
I read that. but while executing tpbconv i did
not see where i can specify that i do not want
solvent?
Thanks
Kavya
On Thu, Jul 12, 2012 at 5:47 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 7/12/12 8:15 AM, Kavyashree M wrote:
Dear Sir,
I had a problem again during g_saltbr calculation
Ok may be i need to specify an index file. I will try that.
And regarding the WARNING: this .tpx file is not fully functional.
I hope it will work fine enough to finish g_saltbr calculation?
Thanks
Kavya
On Thu, Jul 12, 2012 at 5:59 PM, Kavyashree M hmkv...@gmail.com wrote:
I read
Dear Sir,
Thank you It worked :). a very usefull suggestion.
But it did not promt to choose any option. I used
index file.
Thank you
Kavya
On Thu, Jul 12, 2012 at 6:02 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 7/12/12 8:31 AM, Kavyashree M wrote:
Ok may be i need to specify an index
Dear user,
I simulated a homodimer of 238aa each with oplsaa forcefield
using gromacs-4.5.3. But while calculating the rmsf plot I got a
plot in which starting and ending residue were connected by a
straight line along with the actual rmsf plot. Also the two rmsf
plots that it gave were slightly
Dear Users,
I was trying to run a simulation (gromacs4.5.3)
on a Bluegene/L machine. But I was unable to run.
System admin say that I need to change the input
file. I am not sure what needs to be changed in the
input file which specifies no. of nodes usage.
I am not familiar with the bluegene
but it was giving error for not having sufficient data for
512 nodes.
I have run the same job on 8 nodes in i7 machine.
Thank you
With Regards
Kavya
On Mon, Oct 31, 2011 at 5:47 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M wrote:
Dear Users,
I was trying to run a simulation (gromacs4.5.3
Hello,
Thank you. I got the point but I have a doubt,
equilibrate under NPT until the pressure and
temperature are stable, then switch to NVT to
eliminate the boiling issue, how exactly it will
eliminate the boiling issue if we dont use higher
pressure while equlibrating? (as you said that
it is
Ok Thanks.
On Tue, Oct 18, 2011 at 4:41 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M wrote:
Hello,
Thank you. I got the point but I have a doubt,
equilibrate under NPT until the pressure and
temperature are stable, then switch to NVT to
eliminate the boiling issue, how
Dear users,
For simulating a protein at high temperature (more than 300K,
less than 400K) using OPLSAA forcefield, what are the parameters
other than Temperature that need to be taken care of?
Does the energy minimization step also needs to be done at high
temperature? (here my aim is not to
.
Only during equilibration
(NVT and NPT) we use high temperature for maintaining proper density
before starting the final production run.
On Mon, Oct 17, 2011 at 15:15, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
For simulating a protein at high temperature (more than 300K,
less than
, Kavyashree M hmkv...@gmail.com
mailto:hmkv...@gmail.com wrote:
Dear users,
For simulating a protein at high temperature (more than 300K,
less than 400K) using OPLSAA forcefield, what are the parameters
other than Temperature that need to be taken care of?
Does
17, 2011 at 17:04, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M wrote:
Thank you,
What about the pressure that need to be used at that temperature
(for a system of a protein in tip4p water)
The set pressure should reflect whatever system you are trying to model
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