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
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
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
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,
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
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
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
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
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
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
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
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
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,
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
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,
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 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,
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,
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,
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,
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
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 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
-- 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,
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
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,
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
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,
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
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,
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
, 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,
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
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 wanted to know when DEFINE = -DFLEXIBLE has to be used.
its given in the manual that it has to be used when we require flexible
water instead of rigid waters, so if I am using tip4p water model and
OPLSAA force field, and i use DFLEXIBLE option in EM and not in
position MD, is
Thanks
With Regards
Kavya
On Tue, May 10, 2011 at 5:32 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Kavyashree M wrote:
Dear users,
I wanted to know when DEFINE = -DFLEXIBLE has to be used.
its given in the manual that it has to be used when we require flexible
water instead
Dear users,
I was running an MD in a system with 8 cores, for some
reasons I had to shift the job to another system with
same OS and gromacs version. After I started runnning
it said
Gromacs binary or parallel settings not identical to previous run.
Continuation is exact, but is not
Dear users,
I was running an MD in a machine with 2 quad core processors
using all 8 cores system cores, for some reasons I had to shift the
job to another machine with 2 quad cores processors, identical OS
and gromacs version using 8 cores. After I started runnning using check
point
file
Respected Sir,
So that number doesnt mean what it says!
Thanking you
With regards
kavya
On Wed, May 11, 2011 at 4:27 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 11/05/11, *Kavyashree M * hmkv...@gmail.com wrote:
Dear users,
I was running an MD in a machine with 2 quad core
Dear users,
I ran a simulation of a protein in water with rlist = rcoloumb = 1.4nm,
rvdw = 1.0nm, with PME and the distance between in the periodic
was set to a minimum of 2.0 i.,e distance between protein and cell
edge was set to 1.0nm, Even then, when I ran g_mindist, there was
a message
Hello sir,
I had used a dodecahedron cell for simulation. I have run
the simulation for 100ns, did you man I have to restart the
simulation again?
Thanking you
Kavya
On Sun, May 29, 2011 at 5:40 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Kavya,
shortest periodic distance is 1.39714
Hello Sir,
I saw the 21824th frame, it dint look unusually stretched when
I superposed against the initial pdb file. there atoms were hydrogen
atoms of two lysine residues.. And in the entire strttch of 100ns simulation
this is the only periodic image interaction observed, Is it possible to
will this effect the results of the
simulations?
Kindly let me know whether I need to redo the simulation again? or is there
any way to correct this or can it be ignored?
Thanking you
With regards
M. Kavyashree
On Mon, May 30, 2011 at 10:36 AM, Kavyashree M hmkv...@gmail.com wrote:
Hello sir
30, 2011 at 12:24 PM, Kavyashree M hmkv...@gmail.com wrote:
Hello Sir,
The difference between the rcolumb (1.4nm) and minimum image distance
that was obtained between two hydrogen HZ2 and HZ3 atoms of 2 lysine
residues (1.39714nm) is 0.00286nm = 0.0286Ang,
Since this distance is smaller
Dear users,
I was using g_covar (gmx 4.5.3) to find the eigenvalue and
eigenvectors. When I used for protein which is actually - 3740 in
number, it gave a total of 11220 eigenvalues, similarly for bacbone,
c-alpha atoms, the number of eigenvalues given was not matching
with the number of
, 2011 at 2:44 PM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
I was using g_covar (gmx 4.5.3) to find the eigenvalue and
eigenvectors. When I used for protein which is actually - 3740 in
number, it gave a total of 11220 eigenvalues, similarly for bacbone,
c-alpha atoms
Dear users,
I wanted to ensure that the option of -pbc in trjconv is only for
visualization,
and if I do all possible calculations with the original .xtc file there wont
be any
problem.
Thank you
With regards
M. Kavyashree
--
gmx-users mailing listgmx-users@gromacs.org
-- Forwarded message --
From: Mark Abraham mark.abra...@anu.edu.au
Date: Fri, Jun 3, 2011 at 12:58 PM
Subject: Re: [gmx-users] option -pbc in trjconv
To: Discussion list for GROMACS users gmx-users@gromacs.org
On 3/06/2011 3:42 PM, Kavyashree M wrote:
Dear users,
I wanted
Dear Gromacs users,
I am new to essential dynamics, I have gone through
some fundamentals in PCS, the mailing list related to ED
and few publications by -
Amadei (Proteins, 17, 412-425, 1993),
a. Amadei (journal of biomolecular structure and dynamics, 13, 615, 1996)
b. Berk Hess (Physical
Dear Sir,
Thanks for giving a clearer picture about essential dynamics. I was very
eagerly awaiting for a reply. Thanks you very much :).
No, ED does not make any assumptions on the nature of motions. It does
not distinguish anharmonic from harmonic motions. It also does not
distinguish
Dear Sir,
Thanks sir. I will go through them. However I have referred -
A Tutorial on Principle component Analysis by Lindsay I Smith.
Which gave a good understanding about the concepts. Still I
have some doubts regarding eigen values, as you have told
I will think over them again.
But one
Dear Sir,
Ok Sir thanks.
Thanking you
With Regards
M. Kavyashree
On Tue, Jun 7, 2011 at 10:47 AM, Ran Friedman ran.fried...@lnu.se wrote:
From: Tsjerk Wassenaar tsje...@gmail.com
Subject: Re: [gmx-users] Essential dynamics - concepts
To: Discussion list for GROMACS users
Dear Sir,
Thank you Sir for the clarification.
Need to explore about this.
Thanking you
With Regards
M. Kavyashree
On Wed, Jun 8, 2011 at 2:35 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Kavya,
Thanks sir. I will go through them. However I have referred -
A Tutorial on Principle
Dear users,
I have some basic doubts regarding analysis of data:
1. Can the .xtc file from MD be used directly for analysis
without applying -pbc nojump or mol option? [I had
asked the same question before but was not clear
with the answer.
2. While calculating the RMSIP
Dear Sir,
Thank you sir for the clarification. But if there is only one
polymer (protein) with water in the system then also is it
necessary because in one of the mails -
http://lists.gromacs.org/pipermail/gmx-users/2010-October/055320.html
there was a discussion regarding this topic. So I
Dear Sir,
Thanks for your patient reply Sir.
With Regards
M. Kavyashree
On Sat, Jun 11, 2011 at 9:57 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Kavya,
It is absolutely necessary that the molecules be whole, and in the
case of multimers, correctly assembled.
But if there is
Dear users,
While analyzing an MD simulation run for 100ns, for temperature,
pressure, volume and density, I got an output like this -
Energy Average Err.Est. RMSD Tot-Drift
---
Dear Sir,
g_mindist analysis showed the violation of minimum image convention, it
was violated over a short period of time and then it came back to normal.
I attach the plot herewith. Should this data be discarded or any useful
information
can be obtained.
Thank you
With Regards
M. Kavyashree
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