from:"Kavyashree M"

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 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 -contact -r 0.4 -hbm
 matrix-sb.xpm -hbn index-sb.ndx -num num-sb.xvg -b 4000 -e 5

 Is this approach correct?

 Thank you
 Kavya

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Re: [gmx-users] Re: Salt bridge Calculations

Sir,

Thank you very much for your reply. I wanted to calculate
Salt bridge in the whole protein so i am not mentioning the
residues involved. The problem with g_saltbr was that if I
have to calculate the accessibility of these atoms it will be
a problem because it gives the charge groups but not exact
atoms.

This is the reason I thought of using g_hbond. But I wanted
clarification from experts in using this method.

So Is there any problem if I use g_hbond?

Thank you
kavya



On Tue, Apr 2, 2013 at 9:03 PM, bipin singh bipinel...@gmail.com wrote:

 You can use g_dist with specific atoms 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
 
 
  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 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 -contact -r 0.4 -hbm
  matrix-sb.xpm -hbn index-sb.ndx -num num-sb.xvg -b 4000 -e 5
 
  Is this approach correct?
 
  Thank you
  Kavya
 
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Re: [gmx-users] Re: Salt bridge Calculations

Sir,

This g_hbond will generate a matrix similar to
what g_saltbr would have given in terms of variation
of distance between two charge groups.

I want to find out the variation of all the salt bridges
in the protein over the trajectory, if I have to use g_dist
with an index of positive atoms and another of negative
atoms, then it will calculate the distance between the
centre of mass of these two groups.. according to manual.

So How can I use g_dist for this kind of calculation.
I am little confused.

If I take a cut of of 0.4nm (as we mention in g_saltbr), will
it be wrong if I have 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 wanted to calculate
Salt bridge in the whole protein so i am not mentioning the
residues involved. The problem with g_saltbr was that if I
have to calculate the accessibility of these atoms it will be
a problem because it gives the charge groups but not exact
atoms.

This is the reason I thought of using g_hbond. But I wanted
clarification from experts in using this method.

So Is there any problem if I use g_hbond?

Does this really give you any useful information? You'll get an output
file with putative contacts derived from an arbitrary cutoff for any
possible positive-negative pair defined in the index group. I think the
g_dist approach is far more useful and gives you exact insight into
specific pairs. It takes a bit more prep work, but looping the
calculations is trivial to do to make them efficient.

-Justin

Thank you
kavya

On Tue, Apr 2, 2013 at 9:03 PM, bipin singh bipinel...@gmail.com wrote:

You can use g_dist with specific atoms 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

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 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 -contact -r 0.4 -hbm
matrix-sb.xpm -hbn index-sb.ndx -num num-sb.xvg -b 4000 -e 5

Is this approach correct?

Thank you
Kavya

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Re: [gmx-users] Re: Salt bridge Calculations

Sir,

Thank you for the detailed insight. As you mentioned
It does not give much information. But the matrix that
it would generate would only show whether a specific
salt bridge (SB) exited at a given time within the cut-off (0.4).

I got your explanation. Yes water mediated SBs are also
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 a matrix similar to
  what g_saltbr would have given in terms of variation
  of distance between two charge groups.
 
 
 I suppose, in that sense, the output can be useful.


  I want to find out the variation of all the salt bridges
  in the protein over the trajectory, if I have to use g_dist
  with an index of positive atoms and another of negative
  atoms, then it will calculate the distance between the
  centre of mass of these two groups.. according to manual.
 
 
 Yes, but that's not what I suggested you do.  You would need an index group
 for each residue individually, not all negative atoms and all positive
 atoms.  That would definitely be useless.  If you consider each residue
 individually, you can get a very detailed look at what's going on.  What
 you're doing now is saying a salt bridge exists if N and O atoms are
 within 0.4 nm.  Is that an accurate descriptor?  Upon what precedent have
 you based that assessment?  g_dist will also show you frames where those
 atoms may not be within 0.4 nm, but what about the case of water-mediated
 interactions; are those not interesting, as well?  What I think you should
 be doing is approaching the problem from multiple perspectives to get a
 real look at what's going on.

 -Justin


  So How can I use g_dist for this kind of calculation.
  I am little confused.
 
  If I take a cut of of 0.4nm (as we mention in g_saltbr), will
  it be wrong if I have 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 wanted to calculate
   Salt bridge in the whole protein so i am not mentioning the
   residues involved. The problem with g_saltbr was that if I
   have to calculate the accessibility of these atoms it will be
   a problem because it gives the charge groups but not exact
   atoms.
  
   This is the reason I thought of using g_hbond. But I wanted
   clarification from experts in using this method.
  
   So Is there any problem if I use g_hbond?
  
  
   Does this really give you any useful information?  You'll get an output
   file with putative contacts derived from an arbitrary cutoff for any
   possible positive-negative pair defined in the index group.  I think
 the
   g_dist approach is far more useful and gives you exact insight into
   specific pairs.  It takes a bit more prep work, but looping the
   calculations is trivial to do to make them efficient.
  
   -Justin
  
  
Thank you
   kavya
  
  
  
   On Tue, Apr 2, 2013 at 9:03 PM, bipin singh bipinel...@gmail.com
  wrote:
  
You can use g_dist with specific atoms 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
  
  
   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 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 -contact -r 0.4 -hbm
   matrix-sb.xpm -hbn index-sb.ndx -num num-sb.xvg -b 4000 -e 5
  
   Is this approach correct?
  
   Thank you
   Kavya
  
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[gmx-users] Salt bridge Calculations

2013-04-01 Thread Kavyashree M

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 -contact -r 0.4 -hbm
matrix-sb.xpm -hbn index-sb.ndx -num num-sb.xvg -b 4000 -e 5

Is this approach correct?

Thank you
Kavya
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Re: [gmx-users] Free energy landscape by g_sham

2013-03-31 Thread Kavyashree M

Thank you Sir

Regards
kavya


On Sun, Mar 31, 2013 at 11:58 AM, bipin singh bipinel...@gmail.com wrote:

 g_sham calculates free energy landscapes by computing the joint
 probability distribution from the two dimensional plane constructed
 using two quantities (in your case it will be rmsd and radius of
 gyration). Conformations sampled during the simulation were projected
 on this two dimensional plane, and the number of points occupied by
 each cell was counted. The grid cell containing the maximum number of
 points is then assigned as the reference cell, with a free energy
 value of zero. Free energies for all the other cells were assigned
 with respect to this reference cell using the following equation:

 ΔG = -kbT ln P(x,y)/Pmin

 P(x,y) is the estimate of probability density function obtained from a
 histogram of MD data and  Pmin is the maximum of the probability
 density 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,
  rmsd and radius of gyration.
  Any references are welcome.
 
  Thank you
  with Regards
  Kavya
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[gmx-users] Free energy landscape by g_sham

2013-03-30 Thread Kavyashree M

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
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[gmx-users] Hydrophobic contact cut-off

2013-03-26 Thread Kavyashree M

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
useful.

Thank you
Kavya
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Re: [gmx-users] Hydrogen bonding differences

2013-03-22 Thread Kavyashree M

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 Sir,

 Sure I will try with 4.6. presently I am not able to download it.

 Thank you
 kavya


 On Fri, Jan 25, 2013 at 4:04 PM, Erik Marklund er...@xray.bmc.uu.sewrote:

 There were a handful of bugfixes to g_hbond over the last year. Could you
 try 4.6 or a smoking hot 4.5.5? I recognize 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 then it will
 be counted twice in another, So wont the result with/without
 nomerge 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 for a simulation, it
 was found that the average number of intra protein
 hbonds was not equal to sum of MM, MS and SS
 hydrogen bonds. (MM - main chain - main chain,
 MS - main chain - side chain and side chain - side
 chain hydrogen bonds). There was a difference of 5
 or so hbonds between intra-protein and MM+MS+SS
 hbonds. why is this so?
 I selected the options 7 7 for MM, 7 8 for MS and 8 8
 for SS hydrogen bonds.

 One clarification. nhbdist option gives 0, 1, 2, 3 and
 total hydrogen bonds per hydrogen. Does this mean
 that a single hydrogen involving in forming hbond with
 2 different acceptors/donors at different points of time
 in the trajectory.

 Thanks
 kavya
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Re: [gmx-users] Hydrogen bonding differences

2013-03-22 Thread Kavyashree M

Sir,

I tried -nomerge. It is fine now. But will it be wrong to
calculate without nomerge option?

Thank you
Kavya

On Fri, Mar 22, 2013 at 9:28 PM, Erik Marklund er...@xray.bmc.uu.se wrote:

 I could see how -merge (on by default) could lead to this. Have you tried
 -nomerge?

 Erik


 On Mar 22, 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, Kavyashree M hmkv...@gmail.com wrote:

  Dear Sir,

 Sure I will try with 4.6. presently I am not able to download it.

 Thank you
 kavya


 On Fri, Jan 25, 2013 at 4:04 PM, Erik Marklund er...@xray.bmc.uu.se
 wrote:

  There were a handful of bugfixes to g_hbond over the last year. Could
 you
 try 4.6 or a smoking hot 4.5.5? I recognize 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 then it will
 be counted twice in another, So wont the result with/without
 nomerge 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 for a simulation, it
 was found that the average number of intra protein
 hbonds was not equal to sum of MM, MS and SS
 hydrogen bonds. (MM - main chain - main chain,
 MS - main chain - side chain and side chain - side
 chain hydrogen bonds). There was a difference of 5
 or so hbonds between intra-protein and MM+MS+SS
 hbonds. why is this so?
 I selected the options 7 7 for MM, 7 8 for MS and 8 8
 for SS hydrogen bonds.

 One clarification. nhbdist option gives 0, 1, 2, 3 and
 total hydrogen bonds per hydrogen. Does this mean
 that a single hydrogen involving in forming hbond with
 2 different acceptors/donors at different points of time
 in the trajectory.

 Thanks
 kavya
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Re: [gmx-users] Hydrogen bonding differences

2013-03-22 Thread Kavyashree M

Thank you Sir for clarifying the confusion.

Regards
kavya

On Fri, Mar 22, 2013 at 11:18 PM, Erik Marklund er...@xray.bmc.uu.sewrote:

I wouldn't say wrong, but I realized that some residue may make two hbonds
to different parts of the protein, i.e. to the main chain and to a side
chain 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 -nomerge. It is fine now. But will it be wrong to
calculate without nomerge option?

Thank you
Kavya

On Fri, Mar 22, 2013 at 9:28 PM, Erik Marklund er...@xray.bmc.uu.se
wrote:

I could see how -merge (on by default) could lead to this. Have you tried
-nomerge?

Erik

On Mar 22, 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, Kavyashree M hmkv...@gmail.com
wrote:

Dear Sir,

Sure I will try with 4.6. presently I am not able to download it.

Thank you
kavya

On Fri, Jan 25, 2013 at 4:04 PM, Erik Marklund er...@xray.bmc.uu.se

wrote:

There were a handful of bugfixes to g_hbond over the last year. Could

you
try 4.6 or a smoking hot 4.5.5? I recognize 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 then it will
be counted twice in another, So wont the result with/without
nomerge 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 for a simulation, it
was found that the average number of intra protein
hbonds was not equal to sum of MM, MS and SS
hydrogen bonds. (MM - main chain - main chain,
MS - main chain - side chain and side chain - side
chain hydrogen bonds). There was a difference of 5
or so hbonds between intra-protein and MM+MS+SS
hbonds. why is this so?
I selected the options 7 7 for MM, 7 8 for MS and 8 8
for SS hydrogen bonds.

One clarification. nhbdist option gives 0, 1, 2, 3 and
total hydrogen bonds per hydrogen. Does this mean
that a single hydrogen involving in forming hbond with
2 different acceptors/donors at different points of time
in the trajectory.

Thanks
kavya
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[gmx-users] query regarding mk_angndx

2013-03-09 Thread Kavyashree M

-- 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 was:
mk_angndx  -s  a.tpr  -n  angle.ndx   -type   dihedral
output angle.ndx read like this -
[ Phi=180.0_2_43.93 ]
 52018192237353627323031
395957586176747566716970
...

According to my understanding the numbers indicate the 4 atoms
defining the particular dihedral angle.
But when I checked the pdb file for these atoms-
ATOM  5  CA  MET A   1 111.430  40.170 113.130  1.00  0.00
ATOM 18  C   MET A   1 112.060  41.020 112.030  1.00  0.00
ATOM 19  O   MET A   1 111.910  42.240 112.010  1.00  0.00
ATOM 20  N   GLN A   2 112.940  40.430 111.220  1.00  0.00

I could not make out how this defines phi?
Kindly clarify my confusion.

Thank you
kavya
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[gmx-users] query regarding mk_angndx

2013-03-08 Thread Kavyashree M

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
395957586176747566716970
...

According to my understanding the numbers indicate the 4 atoms
defining the particular dihedral angle.
But when I checked the pdb file for these atoms-
ATOM  5  CA  MET A   1 111.430  40.170 113.130  1.00  0.00
ATOM 18  C   MET A   1 112.060  41.020 112.030  1.00  0.00
ATOM 19  O   MET A   1 111.910  42.240 112.010  1.00  0.00
ATOM 20  N   GLN A   2 112.940  40.430 111.220  1.00  0.00

I could not make out how this defines phi?
Kindly clarify my confusion.

Thank you
kavya
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Re: [gmx-users] g_hbond and contact

2013-03-05 Thread Kavyashree M

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 no. of contact/atom had increased
in S2 while the no. of contact/time decreased?

Its a bit confusing though!

Thank you
kavya

On Tue, Mar 5, 2013 at 2:26 PM, Erik Marklund er...@xray.bmc.uu.se wrote:

 To clarify: the -hbn output is not very indicative of how many contacts
 there were since some of them could be present in one frame but absent in
 99. The -num option, however, provides the number of contacts over
 time, and its time average probably tells you much more in this case.

 What version of g_hbond are you using? I remember there were several
 bugfixes over the last 6 months or so. With the latest version(s) I believe
 that the -merge flag has no effect on contact analysis, which is correct.

 Erik


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Re: [gmx-users] g_hbond and contact

2013-03-05 Thread Kavyashree M

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 a contact with an
atom only in once or all the time, in the whole trajectory, it will be
mentioned.
Am I right?

Yes.

So from the problem I had, can I say that no. of contact/atom had
increased
in S2 while the no. of contact/time decreased?

That depends. If 'contact' means unique interactions and 'atom' means e.g.
all atoms in in your system, then yes.

Its a bit confusing though!

Thank you
kavya

On Tue, Mar 5, 2013 at 2:26 PM, Erik Marklund er...@xray.bmc.uu.se
wrote:

To clarify: the -hbn output is not very indicative of how many contacts
there were since some of them could be present in one frame but absent in
99. The -num option, however, provides the number of contacts over
time, and its time average probably tells you much more in this case.

What version of g_hbond are you using? I remember there were several
bugfixes over the last 6 months or so. With the latest version(s) I
believe
that the -merge flag has no effect on contact analysis, which is correct.

Erik

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[gmx-users] g_hbond and contact

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 that the number of contacts was more in 2nd simulation
compared to
the first. But When I compared xvg file it was showing the opposite
behaviour.
The contacts was also calculated using g_mdmat for the same cutoff and it
was agreeing
with the numbers I got from in index output of g_hbond.

Why is this difference in index and xvg output?
Also the xvg file looks like -

s0 legend Contacts
@ s1 legend Pairs within 0.4 nm
  40007496   0
  40027513   0
  40047605   0
  40067531   0
  40087573   0
  40107546   0
  40127544   0
  40147526   0
  40167530   0
  40187496   0
  40207526   0
..


Thank you
kavya
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Re: [gmx-users] g_hbond and contact

Sir,

From Index file which gives the unique contacts -
First section the list of atoms I want to analyse
[ C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_CZ2_CZ3_CH2 ]

second section : the unique contacts of each atoms with others
[ contacts_C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_CZ2_CZ3_CH2 ]
5 7ws
5 10
5 14
5 18
5 22
5 24
5 27
5 30
5 35
5292
5296
530

From this second section Total contacts was extracted for each atom and
compared with
that from a second simulation.
These contacts was matching with the contacts of the 3rd column from
g_mdmat output -
@ legend string 0 Total/mean
@ legend string 1 Total
@ legend string 2 Mean
@ legend string 3 # atoms
@ legend string 4 Mean/# atoms
#resratio tot mean natm mean/atm
1 1.001 1110.991110.991
2 1.244 10 8.0411 8.041
3 1.166 1311.147111.147
4 1.036 1110.615110.615

While the time dependent contacts in the xvg file shows that the first
simulation has more
contacts than the second one..

I hope I am clear this time.

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 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 that the number of contacts was more in 2nd simulation
compared to
the first. But When I compared xvg file it was showing the opposite
behaviour.

These statements don't make any sense. How did you determine that the
number of contacts in simulation 2 was greater than simulation 1, but then
the .xvg files showed the opposite? The number of contacts come from the
.xvg files? Perhaps you simply swapped your files during analysis.

The contacts was also calculated using g_mdmat for the same cutoff and it
was agreeing
with the numbers I got from in index output of g_hbond.

Why is this difference in index and xvg output?

An index group is a list of atom numbers. The .xvg output is whatever you
tell it to be, in this case, the number of contacts within the group
selected.

-Justin

Also the xvg file looks like -

s0 legend Contacts
@ s1 legend Pairs within 0.4 nm
40007496 0
40027513 0
40047605 0
40067531 0
40087573 0
40107546 0
40127544 0
40147526 0
40167530 0
40187496 0
40207526 0
..

Thank you
kavya

--
==**==

Re: [gmx-users] g_hbond and contact

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
The command I gave -
g_hbond_46  -fx.xtc-s   x.tpr-contact   -n   x.ndx   -r   0.4
-hbm   o.xpm   -hbn   o.ndx   -num   o.xvg
my index file contained a group of hydrophobic atoms. which I supplied in
the x.ndx.



  You don't define contacts in an index group, you define atoms that may or
 may not make contacts with others.


The one I mentioned here is the output index file from the g_hbond (4.6
version) - o.ndx.



  [ contacts_C_CA_CB_CD_CD1_CD2_**CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_**CZ2_CZ3_CH2
 ]
5  7ws
5 10
5 14
5 18
5 22
5 24
5 27
5 30
5 35
5292
5296
530


 There's something very wrong with this index file.  How did you generate
 it? The presence of a repeated atom number (5) and a nonsensical one (7ws)
 leads me to believe that you've done something incorrect.  Did this come
 from g_hbond? It looks like the output of -hbn, which is only useful for
 decoding hbmap.xpm, nothing else.


I did not generate this. The tool (g_hbond) generated this index file. It
is the -hbn output.



  From this second section Total contacts was extracted for each atom and

 compared with
 that from a second simulation.
 These contacts was matching with the contacts of the 3rd column from
 g_mdmat output -
 @ legend string 0 Total/mean
 @ legend string 1 Total
 @ legend string 2 Mean
 @ legend string 3 # atoms
 @ legend string 4 Mean/# atoms
 #resratio  tot  mean  natm  mean/atm
1 1.001   1110.991110.991
2 1.244   10 8.0411 8.041
3 1.166   1311.147111.147
4 1.036   1110.615110.615


 While the time dependent contacts in the xvg file shows that the first
 simulation has more
 contacts than the second one..


 That shouldn't be unexpected.  Two independent simulations have no
 guarantee of doing the same thing, that's why sampling is so important.


Thank you
kavya
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Re: [gmx-users] g_hbond and contact

I am sorry There is no 7ws Its a typographic error. What I wanted to ask
was -
I am comparing two simulations S1 and S2 for contacts at a given cut off
I used g_mdmat and g_hbond to calculate it.
g_hbond outputs: of -num and -hbn was considered.
1. -hbn output was analysed to calculate how many contacts each
atom has from both S1 and S2.
2. -num output graph was compared from both S1 and S2.
g_mdmat output: of -no was considered.
3. -no output was analysed from both S1 and S2 using the
third column or the second Y value which gives total
contacts
of each atom.

It was observed that 1 and 3 matched exactly giving the same number of
contacts each atom has (in the whole simulations). indicating that the
number
of contacts each atom has was more in S2 than S1.

But the graph from 2 indicated that the number of contacts (along the
trajectory)
in S1 was higher than S2.

My doubt is:
The number of contact per atom follows S2 S1
while number of contacts per time follows S1 S2.
I am unclear as to what I have to conclude from this observations.

- I used the same cutoff throughout.
- There has 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 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
The command I gave -
g_hbond_46 -fx.xtc-s x.tpr-contact -n x.ndx -r 0.4
-hbm o.xpm -hbn o.ndx -num o.xvg
my index file contained a group of hydrophobic atoms. which I supplied in
the x.ndx.

You don't define contacts in an index group, you define atoms that may
or
may not make contacts with others.

The one I mentioned here is the output index file from the g_hbond (4.6
version) - o.ndx.

[ contacts_C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_***
*CZ2_CZ3_CH2

]
5 7ws
5 10
5 14
5 18
5 22
5 24
5 27
5 30
5 35
5292
5296
530

There's something very wrong with this index file. How did you
generate
it? The presence of a repeated atom number (5) and a nonsensical one
(7ws)
leads me to believe that you've done something incorrect. Did this come
from g_hbond? It looks like the output of -hbn, which is only useful for
decoding hbmap.xpm, nothing else.

I did not generate this. The tool (g_hbond) generated this index file.
It
is the -hbn output.

OK, then I still don't know what 7ws is, but the only purpose for this
file is to provide a key to the existence matrix in hbmap.xpm. Your
previous description indicated that you were using it for some other
analysis, which would not be appropriate.

The other thing worth mentioning here is something that was posted to the
list just a few hours ago, that the output of g_hbond -contact may not
agree with other methods of calculating contacts, especially in the case of
-merge vs. -nomerge.

-Justin

From this second section Total contacts was extracted for each atom and

compared with
that from a second simulation.
These contacts was matching with the contacts of the 3rd column from
g_mdmat output -
@ legend string 0 Total/mean
@ legend string 1 Total
@ legend string 2 Mean
@ legend string 3 # atoms
@ legend string 4 Mean/# atoms
#resratio tot mean natm mean/atm
1 1.001 1110.991110.991
2 1.244 10 8.0411 8.041
3 1.166 1311.147111.147
4 1.036 1110.615110.615

While the time dependent contacts in the xvg file shows that the first
simulation has more
contacts than the second one..

That shouldn't be unexpected. Two independent simulations have no
guarantee of doing the same thing, that's why sampling is so important.

Thank you
kavya

--
==**==

[gmx-users] order in index and matrix

2013-02-21 Thread Kavyashree M

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
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[gmx-users] Number of interactions per residue

2013-02-14 Thread Kavyashree M

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
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Re: [gmx-users] Number of interactions per residue

2013-02-14 Thread Kavyashree M

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 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
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[gmx-users] Re: Salt-bridge segmentation fault

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 users,

 While calculating salt bridges using g_saltbr I got
 segmentation fault when I used trajectory with only
 the protein. But when I used the trajectory with
 water It worked. But the problem was that the
 monomers were far apart in the trajectory with water
 and not with the only-protein trajectory.

 Kindly help!

 Thank you
 Kavya


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Re: [gmx-users] Re: Regarding mean square displacement

Dear Sir,

Thank you for the reply,

It does not cross the boundary. I made the trajectory
so that the dimers are together.

I again calculated on a superposed trajectory, Then I
got MSDs in the range of 0.01 to 0.15nm^2. But this
is still higher than the value mentioned in the paper 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 for this. I checked the structure it is not denatured,
 In addition I used -rmcomm in order to remove the COM movements.


 Sounds like a PBC issue.  Does your dimer split across periodic
 boundaries?  If it does, then your MSD is going to go through the roof
 because it's measuring the MSD of the whole protein.

 -Justin

  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 MSD? As the values given in a
 paper i was referring was in Ang^2
 J. Chem. Theory Comput. 2012, 8, 1129-1142


 Command that i used -

 echo 3 3 |g_msd -f a.xtc -s a.tpr -o a.xvg -n a.ndx -trestart 10 -b 4000
 -e 5 -rmcomm

 Is the range of diffusion coefficient of proteins of in water l
 in the range of x e-5 cm^2/s? (hemoglobin is 0.1 e-5 cm^2/s)

 Thank you
 kavya




 --
 ==**==

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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Re: [gmx-users] Re: Regarding mean square displacement

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 on a dimer for 50ns using OPLS-AA and TIP4P water
model. Using Gromacs4.5.3.
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 that the dimers are together.

 I again calculated on a superposed trajectory, Then I
 got MSDs in the range of 0.01 to 0.15nm^2. But this
 is still higher than the value mentioned in the paper or
 is this acceptable?


 Are you studying the same protein?  Given sparse detail in an email
 thread, not knowing whether the simulations were done correctly or for
 sufficient time, no one can assess correctness here.

 -Justin

  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 for this. I checked the structure it is not denatured,
 In addition I used -rmcomm in order to remove the COM movements.


  Sounds like a PBC issue.  Does your dimer split across periodic
 boundaries?  If it does, then your MSD is going to go through the roof
 because it's measuring the MSD of the whole protein.

 -Justin

   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 MSD? As the values given in a
 paper i was referring was in Ang^2
 J. Chem. Theory Comput. 2012, 8, 1129-1142


 Command that i used -

 echo 3 3 |g_msd -f a.xtc -s a.tpr -o a.xvg -n a.ndx -trestart 10 -b
 4000
 -e 5 -rmcomm

 Is the range of diffusion coefficient of proteins of in water l
 in the range of x e-5 cm^2/s? (hemoglobin is 0.1 e-5 cm^2/s)

 Thank you
 kavya




  --
 ====


 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin
 h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 

 ====

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 --
 ==**==

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 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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Re: [gmx-users] Re: Salt-bridge segmentation fault

Thank you,

I have noticed this in the output of the g_saltbr. Later
I separated the files according to what ever I require.
My worry was only that of the dimeric interface which
could not be seen because it is separated.

I will try by giving a separate tpr file without water.

Thank you
Kavya

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 correct?

Most Gromacs tools handle PBC well for simple metrics like measurements.
I would suspect that the seg fault comes from a mismatch in the .tpr and
.xtc contents. g_saltbr is a rather stupid tool that tries to guess salt
bridges based on anything that's charged, which includes ions and other
groups that don't necessarily participate in such interactions (see the
discussion on this same topic in recent days). Perhaps if g_saltbr is
identifying elements that it wants to examine from the .tpr file but can't
find them in the trajectory, you get a seg fault. This shouldn't happen,
but you can also use tpbconv to produce a subset .tpr file with just the
protein for the purposes of analysis.

-Justin

On Thu, Feb 7, 2013 at 3:39 PM, Kavyashree M hmkv...@gmail.com wrote:

Dear users,

While calculating salt bridges using g_saltbr I got
segmentation fault when I used trajectory with only
the protein. But when I used the trajectory with
water It worked. But the problem was that the
monomers were far apart in the trajectory with water
and not with the only-protein trajectory.

Kindly help!

Thank you
Kavya

--
==**==

Re: [gmx-users] Re: Regarding mean square displacement

Thank you,

My intention is mainly to compare the MSDs of the
trajectory and not the diffusion as such. The paper I
mentioned have used a tetramer for the similar analysis.
Hence I wanted to know whether the values I obtained
is sensible.

Thank you
Kavya

On Thu, Feb 7, 2013 at 7:25 PM, Justin 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 on a dimer for 50ns using OPLS-AA and TIP4P water
 model. Using Gromacs4.5.3.
 If any other information is required Please let me know.


 The specific suitability of a protocol is dependent upon what you believe
 to be correct for your system based on precedent and chemical knowledge.
  Also be aware that post-processing of the trajectory to superimpose frames
 defeats the purpose of measuring diffusion - if you re-center or
 superimpose your structures, it's not diffusing!  Dealing with a dimeric
 protein may be a challenge for which g_msd wasn't designed, so I don't know
 if there's an easy solution here.  Perhaps someone else can suggest
 something.

 -Justin

  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 that the dimers are together.

 I again calculated on a superposed trajectory, Then I
 got MSDs in the range of 0.01 to 0.15nm^2. But this
 is still higher than the value mentioned in the paper or
 is this acceptable?


  Are you studying the same protein?  Given sparse detail in an email
 thread, not knowing whether the simulations were done correctly or for
 sufficient time, no one can assess correctness here.

 -Justin

   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 for this. I checked the structure it is not denatured,
 In addition I used -rmcomm in order to remove the COM movements.


   Sounds like a PBC issue.  Does your dimer split across periodic

 boundaries?  If it does, then your MSD is going to go through the roof
 because it's measuring the MSD of the whole protein.

 -Justin

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 MSD? As the values given in a
 paper i was referring was in Ang^2
 J. Chem. Theory Comput. 2012, 8, 1129-1142


 Command that i used -

 echo 3 3 |g_msd -f a.xtc -s a.tpr -o a.xvg -n a.ndx -trestart 10 -b
 4000
 -e 5 -rmcomm

 Is the range of diffusion coefficient of proteins of in water l
 in the range of x e-5 cm^2/s? (hemoglobin is 0.1 e-5 cm^2/s)

 Thank you
 kavya




   --

 ==**==



 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin**
 http://vt.edu/Pages/Personal/**justinhttp://vt.edu/Pages/Personal/justin
 
 h**ttp://www.bevanlab.**biochem.vt.**edu/Pages/**Personal/justin
 http://www.**bevanlab.biochem.vt.edu/Pages/**Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 



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[gmx-users] Regarding mean square displacement

2013-02-06 Thread Kavyashree M

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 Comput. 2012, 8, 1129-1142

Command that i used -

echo 3 3 |g_msd -f a.xtc -s a.tpr -o a.xvg -n a.ndx -trestart 10 -b 4000 -e
5 -rmcomm

Is the range of diffusion coefficient of proteins of in water l
in the range of x e-5 cm^2/s? (hemoglobin is 0.1 e-5 cm^2/s)

Thank you
kavya
-- 
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[gmx-users] Re: Regarding mean square displacement

2013-02-06 Thread Kavyashree M

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 for this. I checked the structure it is not denatured,
In addition I used -rmcomm in order to remove the COM movements.

Kindly reply

Thank you
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 MSD? As the values given in a
 paper i was referring was in Ang^2
 J. Chem. Theory Comput. 2012, 8, 1129-1142

 Command that i used -

 echo 3 3 |g_msd -f a.xtc -s a.tpr -o a.xvg -n a.ndx -trestart 10 -b 4000
 -e 5 -rmcomm

 Is the range of diffusion coefficient of proteins of in water l
 in the range of x e-5 cm^2/s? (hemoglobin is 0.1 e-5 cm^2/s)

 Thank you
 kavya



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Re: [gmx-users] Superimposed trajectory

2013-02-06 Thread Kavyashree M

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 (from each frame) superimposed
  on the first frame using the original traj.xtc file?
 
  Thank you
  kavya
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 --
 Tsjerk A. Wassenaar, Ph.D.

 post-doctoral researcher
 Biocomputing Group
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[gmx-users] Re: clarification regarding contact map - g_mdmat

2013-02-01 Thread Kavyashree M

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
 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 1.000  473   473.0001   473.000
   3 1.000  473   473.0001   473.000
   4 1.000  473   473.0001   473.000
   5 1.000  473   473.0001   473.000
   6 1.000  473   473.0001   473.000
   7 1.000  473   473.0001   473.000
 
 So it mean that on an average each calpha atom contacts all
 other C-alpha atom in the whole trajectory at some point of time.

 In order to cross check it I collected data only for one time frame.
 This was also very similar results. all the residues have a minimum
 of atleast 471 contacts.

 Some one kindly clarify where I am going wrong.? the command
 I used was -
 g_mdmat -f .*.xtc -s *.tpr -no *.xvg -mean *.xpm -b 4000 -e 4000 -t 8.0

 Is this trucating distance in Angstroms or nanometer?

 Thank you
 Kavya


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[gmx-users] clarification regarding contact map - g_mdmat

2013-01-31 Thread Kavyashree M

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 1.000  473   473.0001   473.000
  3 1.000  473   473.0001   473.000
  4 1.000  473   473.0001   473.000
  5 1.000  473   473.0001   473.000
  6 1.000  473   473.0001   473.000
  7 1.000  473   473.0001   473.000

So it mean that on an average each calpha atom contacts all
other C-alpha atom in the whole trajectory at some point of time.

In order to cross check it I collected data only for one time frame.
This was also very similar results. all the residues have a minimum
of atleast 471 contacts.

Some one kindly clarify where I am going wrong.? the command
I used was -
g_mdmat -f .*.xtc -s *.tpr -no *.xvg -mean *.xpm -b 4000 -e 4000 -t 8.0

Is this trucating distance in Angstroms or nanometer?

Thank you
Kavya
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[gmx-users] Distance matrix of the trajectory

2013-01-25 Thread Kavyashree M

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 1.000  640   640.000   1933.684
  2 1.000  530   530.000   1731.176
  3 1.000  805   805.000   2236.591
  4 1.000  571   571.000   1733.588

I am little doubtful about the number under total. Does this mean that the
atoms of that residue has total of 640 contacts (in one frame)?

Are there any otherway to get contact map for the whole trajectory where we
can mention min and max cut-off distance?

Thank you
kavya
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Re: [gmx-users] Hydrogen bonding differences

2013-01-25 Thread Kavyashree M

Dear Sir,

Sure I will try with 4.6. presently I am not able to download it.

Thank you
kavya

On Fri, Jan 25, 2013 at 4:04 PM, Erik Marklund er...@xray.bmc.uu.se wrote:

 There were a handful of bugfixes to g_hbond over the last year. Could you
 try 4.6 or a smoking hot 4.5.5? I recognize 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 then it will
 be counted twice in another, So wont the result with/without
 nomerge 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 for a simulation, it
 was found that the average number of intra protein
 hbonds was not equal to sum of MM, MS and SS
 hydrogen bonds. (MM - main chain - main chain,
 MS - main chain - side chain and side chain - side
 chain hydrogen bonds). There was a difference of 5
 or so hbonds between intra-protein and MM+MS+SS
 hbonds. why is this so?
 I selected the options 7 7 for MM, 7 8 for MS and 8 8
 for SS hydrogen bonds.

 One clarification. nhbdist option gives 0, 1, 2, 3 and
 total hydrogen bonds per hydrogen. Does this mean
 that a single hydrogen involving in forming hbond with
 2 different acceptors/donors at different points of time
 in the trajectory.

 Thanks
 kavya
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Re: [gmx-users] Hydrogen bonding differences

2013-01-24 Thread Kavyashree M

Dear Sir,

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,

Thanks
kavya
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[gmx-users] g_hbond existence matrix

2013-01-24 Thread Kavyashree M

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 addition, the file also contains white coloured o what is
this?

Thank you
Kavya
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Re: [gmx-users] g_hbond existence matrix

2013-01-24 Thread Kavyashree M

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  /* 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 addition, the file also contains white coloured o what is
 this?


 There are only two characters in the .xpm file, a space and an 'o' as you
 noted above.  The font color that appears in your terminal is whatever you
 have set it to be; there is no significance of different colored letters in
 the .xpm file. There either is a hydrogen bond in a frame (in which case
 you see 'o') or there is not (and thus a blank space).

 -Justin

 --
 ==**==

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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[gmx-users] g_saltbr not include side chains of GLU and ASP??

2013-01-03 Thread Kavyashree M

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 chain oxygen atoms of ASP
and GLU was not present in any of  the file. And most of the
atoms that corresponds to the ASP and GLU were CB, CG or
CD.
Kindly someone clarify why is this so.

Thank you
Kavya
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[gmx-users] Re: g_saltbr not include side chains of GLU and ASP??

2013-01-03 Thread Kavyashree M

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 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 chain oxygen atoms of ASP
 and GLU was not present in any of  the file. And most of the
 atoms that corresponds to the ASP and GLU were CB, CG or
 CD.
 Kindly someone clarify why is this so.

 Thank you
 Kavya

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Re: [gmx-users] Re: g_saltbr not include side chains of GLU and ASP??

2013-01-03 Thread Kavyashree M

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:

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

I only took a quick look through the code, but it seems that what g_saltbr
is doing is labeling its output files based on the first atom in a given
charge group. The charge group, not the individual atoms per se, are what
dictate the search criteria. You haven't said which force field you're
using, but I will assume it's one of the Gromos ones, wherein the C[GD]
atom is the first atom in the COO- charge group.

-Justin

Thank you
kavya

On Thu, Jan 3, 2013 at 3:28 PM, Kavyashree M hmkv...@gmail.com 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 chain oxygen atoms of ASP
and GLU was not present in any of the file. And most of the
atoms that corresponds to the ASP and GLU were CB, CG or
CD.
Kindly someone clarify why is this so.

Thank you
Kavya

--
==**==

Re: [gmx-users] g_dih calculation doubt

2012-12-26 Thread Kavyashree M

Thanks both of you for the suggestions.
Regarding the backup files - I did not run the command
multiple times.

Thank you
kavya

On Thu, Dec 27, 2012 at 1:01 AM, Mark Abraham mark.j.abra...@gmail.comwrote:

 Unfortunately, g_dih was written before 1997 and its documentation is very
 poor. It does not actually read the connectivity in the .tpr file, nor does
 it attempt to infer connectivity other than for some protein backbone
 dihedrals. For some reason, it thinks it finds some for your topology, but
 can't find parameters for them (wherever it imagines it should find them).

 As far as I 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 was using g_dih to find the phi/psi transitions of a protein
  along the trajectory using the following command -
  g_dih -f a.xtc -s a.tpr -o dihout.out -b x -e y -w
  When it started running it indicated many of the following lines
  Dihedral around 7793,7804 not found in topology. Using mult=3
  what does it mean..? they are not nearby atoms so as to calculate
  dihedral angle..
 
 
  Clearly g_dih thinks they are.  Refer to your coordinate or topology
 files
  to find out what those atoms are.  A difference of only 11 atoms is not
  very large.  They could indeed be in the same residue or in a disulfide.
 
 
   At the end it gave the dihedral transitions of each residue along the
  trajectory - it displayed -
  Calculated all dihedrals, now analysing...
  and then it took backup of all residue transitions creating new
  xvg files of the same residues. I compared the two files ie, the
  backup file and the corresponding new file there was drastic differences
  why is there difference between these two files although both are
  plots of degrees v/s time.
 
 
  Backup files are generated after multiple invocations of a command.
   Apparently whatever you ran multiple times produced different output.
 
 
   One more question is some times it shows dihedral values of  more
  than 360.. sometimes 1000 etc.. does it mean that the bond has undergone
  rotation so many times.. I am sorry  I am not getting this. Also the
 file
  that it generates does not say which is phi/psi specifically. So I
 suppose
  2nd column is phi and 3rd column is psi? it it right?
 
 
  You'll have to provide snippets of your output, with complete .xvg header
  information here.  Most files are very well labeled so as to make the
  columns obvious.
 
  -Justin
 
  --
  ==**==
 
  Justin A. Lemkul, Ph.D.
  Research Scientist
  Department of Biochemistry
  Virginia Tech
  Blacksburg, VA
  jalemkul[at]vt.edu | (540) 231-9080
  http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
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  ==**==
 
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Re: [gmx-users] g_hbond index

2012-12-19 Thread Kavyashree M

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 in that protein with some unique property.
I wanted to see the variation of Hbond of these residues with the whole
protein. so group 18 is a subset 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 the hydrogen bonding of a group of residues with
 the whole protein so I had an index of this group. When I give the
 option as 18 (index number) and 1 (whole protein), I get several
 messages
 Hm. This isn't the first time I found this donor (...,...)
 But later it does calculates. does this mean that it is double counting
 those interactions?


 What is group 18?  Be mindful of the g_hbond requirement that the chosen
 groups must be completely unique or completely overlapping.

 -Justin

 --
 ==**==

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
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Re: [gmx-users] g_hbond index

2012-12-19 Thread Kavyashree M

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 in that protein with some unique property.
I wanted to see the variation of Hbond of these residues with the whole
protein. so group 18 is a subset of group 1.

You see a difference likely because you are invoking the command
incorrectly (with overlapping index groups) and it is affecting the way the
donor and acceptor arrays are constructed. The proper method of analysis
is to monitor H-bonds within group 18 and then between group 18 and
whatever part of the protein that does not overlap with it.

-Justin

--
==**==

[gmx-users] Re: g_sas : Total surface area

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 residues but summing up to 20 amino acids. Then using
 g_sas calculated sas for these 3 sets separately and whole protein
 separately for the same trajectory.
 I was expecting that the average value of
 Total surface area (protein) ~ Total surface area (A)+Total surface area
 (B)+Total surface area (C)
 But it is not so.
 Could anyone explain me why?

 Thank you
 Kavya

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[gmx-users] Re: g_sas : Total surface area

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 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 residues but summing up to 20 amino acids. Then using
 g_sas calculated sas for these 3 sets separately and whole protein
 separately for the same trajectory.
 I was expecting that the average value of
 Total surface area (protein) ~ Total surface area (A)+Total surface area
 (B)+Total surface area (C)
 But it is not so.
 Could anyone explain me why?

 Thank you
 Kavya



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Re: [gmx-users] g_sas : Total surface area

Thank you very much for your replies.

The system consists of a homodimer in tip4p dodecahedron box
simulated using OPLSAA ff.

The A B C here are the amino acids:
A- S T N Q G P H
B- A V L I M C F Y W
C- D E K R

So these are set in an index file and i used each one of these
to calculate sasa in g_sas.
When the g_sas calculation starts it specifies the number of
hydrophobic atoms, one of the example -
For the whole protein -
4644 out of 7590 atoms were classified as hydrophobic
For group A of same protein -
702 out of 1424 atoms were classified as hydrophobic
For group B of same protein -
2614 out of 3496 atoms were classified as hydrophobic
For group C of same protein -
1328 out of 2670 atoms were classified as hydrophobic

In this the number of hydrophobic atoms of A, B and C adds
up to the total hydrophobic atoms in whole protein.

but after the calculation is over the average values of Total sas
(legend S2 of area.xvg file) of the protein and Total sas of A, B
and C are given below
Whole protein - 254.04nm^(-2)
A - 175.87nm^(-2)
B - 211.33nm^(-2)
C - 264.65nm^(-2)

I expected that the average total sas of Whole protein atleast approximately
equal the sum of Total sas of A, B and C. If not why? All calculations are
done for the same trajectory after equilibrating.

Thank you
Kavya



On Wed, Dec 12, 2012 at 5:20 PM, francesco oteri
francesco.ot...@gmail.comwrote:

 Hi Kavya,
 Can you better describe your system?
 As Mark suggested, could you supply some number?

 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
   exclusive residues but summing up to 20 amino acids. Then using
   g_sas calculated sas for these 3 sets separately and whole protein
   separately for the same trajectory.
   I was expecting that the average value of
   Total surface area (protein) ~ Total surface area (A)+Total surface
 area
   (B)+Total surface area (C)
   But it is not so.
   Could anyone explain me why?
  
 
  Not without seeing any numbers. You're probably thinking that the surface
  area of A excludes the interfacial area to the other sets, but it
 doesn't.
 
  Mark
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Re: [gmx-users] g_sas : Total surface area

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 much for your replies.

The system consists of a homodimer in tip4p dodecahedron box
simulated using OPLSAA ff.

The A B C here are the amino acids:
A- S T N Q G P H
B- A V L I M C F Y W
C- D E K R

So these are set in an index file and i used each one of these
to calculate sasa in g_sas.
When the g_sas calculation starts it specifies the number of
hydrophobic atoms, one of the example -
For the whole protein -
4644 out of 7590 atoms were classified as hydrophobic
For group A of same protein -
702 out of 1424 atoms were classified as hydrophobic
For group B of same protein -
2614 out of 3496 atoms were classified as hydrophobic
For group C of same protein -
1328 out of 2670 atoms were classified as hydrophobic

In this the number of hydrophobic atoms of A, B and C adds
up to the total hydrophobic atoms in whole protein.

but after the calculation is over the average values of Total sas
(legend S2 of area.xvg file) of the protein and Total sas of A, B
and C are given below
Whole protein - 254.04nm^(-2)
A - 175.87nm^(-2)
B - 211.33nm^(-2)
C - 264.65nm^(-2)

I expected that the average total sas of Whole protein atleast
approximately
equal the sum of Total sas of A, B and C. If not why? All calculations are
done for the same trajectory after equilibrating.

Are you selecting the correct groups when running g_sas? For instance,
you should be selecting Protein for the surface calculation, and then
your custom subsets for output. If you use the subsets for both surface
calculation and output, you will get an artificially inflated value that
includes extra surface area that is actually buried in the context of the
whole structure.

-Justin

--
==**==

==**==

Re: [gmx-users] g_sas : Total surface area

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, Justin Lemkul jalem...@vt.edu wrote:

On 12/12/12 9:37 AM, Kavyashree M wrote:

Thank you very much for your replies.

The system consists of a homodimer in tip4p dodecahedron box
simulated using OPLSAA ff.

The A B C here are the amino acids:
A- S T N Q G P H
B- A V L I M C F Y W
C- D E K R

In this the number of hydrophobic atoms of A, B and C adds
up to the total hydrophobic atoms in whole protein.

I expected that the average total sas of Whole protein atleast
approximately
equal the sum of Total sas of A, B and C. If not why? All calculations
are
done for the same trajectory after equilibrating.

-Justin

--
==**==

==**==

Re: [gmx-users] Asymmetry in homo dimer simulation

2012-12-06 Thread Kavyashree M

Sir,

I also have come across several papers where they have done
single simulations but in recent days most of them perform
multiple trajectories for shorter period. But I am not clear how
can multiple trajectories for shorter period of time compensate
for single extended time simulation.

Thank 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 at different time intervals.
  Running multiple simulation is definitely the best suggestion but
  due to time and machine constraint it would be difficult. Instead
  I have two mesophilic simulations. But Is there any other way
  by which I can prove this point?
 
 
  Not using single trajectories.  Your job is to convince reviewers that
 your work is sound.  A single trajectory is not convincing, at least to any
 reviewer that does his or her homework :)
 

 I don't think that the use of single trajectories is necessarily wrong,
 as long as they are sufficiently long. It's usually the amount of sampling
 that is the crucial point, no?

 Erik

  -Justin
 
  --
  
 
  Justin A. Lemkul, Ph.D.
  Research Scientist
  Department of Biochemistry
  Virginia Tech
  Blacksburg, VA
  jalemkul[at]vt.edu | (540) 231-9080
  http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 
  
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 er...@xray.bmc.uu.se
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Re: [gmx-users] Asymmetry in homo dimer simulation

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 is 300K and T2 is 363K the protein
being simulated is from Ecoli (mesophilic).

As you have mentioned I do not have replicates of simulations
hence only one 50ns 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 the chains with same number
of amino acids and in same configuration) using gromacs 453 in
OPLSAA force field at 2 different temperatures (say T1 and T2). It
was noticed that the rms fluctuation of chain A differs from chain B
in both the simulations. In one of the temperature (T2) the rmsf of the
protein is supposed to be more compared to the other (T1).

When I compare rmsf of chain A at T1 with chain A at T2 (similarly for
chain B). I observed that it shows opposite behaviour. ie chainB is
having increased fluctuation at T1 than at T2.

But actually i observed that the fluctuation of chain A at T1 resembles
the fluctuation of chain B at T2 (with increased values) and similarly
the fluctuations of chain B at T1 resembles that of chain A fluctuation
at T2 (with increased values).

Is this possible? or is there anything wrong?

Your results would indicate simply that while one protein subunit
fluctuates more, the other becomes somewhat more rigid. That's plausible,
but perhaps not intuitive. Keep in mind that RMSF is very sensitive to
whether or not your simulations are actually converged, and a single
trajectory under each condition is insufficient to make very solid claims
about anything. How long are the simulations? How much of the initial
time is being disregarded, and thus how long are the equilibrated segments
of the simulations? How different are T1 and T2?

-Justin

--
==**==

Re: [gmx-users] Asymmetry in homo dimer simulation

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,

As you have mentioned I do not have replicates of simulations
hence only one 50ns 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,

When I compare rmsf of chain A at T1 with chain A at T2 (similarly for
chain B). I observed that it shows opposite behaviour. ie chainB is
having increased fluctuation at T1 than at T2.

Is this possible? or is there anything wrong?

-Justin

--
==**==

Re: [gmx-users] Asymmetry in homo dimer simulation

Sir,

Thank you for your suggestions. I decided the cutoff based on
RMSD convergence. I will calculate at different time intervals.
Running multiple simulation is definitely the best suggestion but
due to time and machine constraint it would be difficult. Instead
I have two mesophilic simulations. 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,

I would suggest you compare different, overlapping blocks of time as a
further assessment of convergence. What motivated the choice of the 4-50
ns time frame? Simple RMSD stability? While that may be one way to assess
convergence, it is not necessarily definitive. If you analyze your RMSF
results over different times, i.e. 4-50, 10-50, 20-50, etc, how do they
compare?

As you have mentioned I do not have replicates of simulations
hence only one 50ns simulation per temperature.

I would encourage you to run more simulations. One trajectory is not
definitive.

-Justin

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,

When I compare rmsf of chain A at T1 with chain A at T2 (similarly for
chain B). I observed that it shows opposite behaviour. ie chainB is
having increased fluctuation at T1 than at T2.

Is this possible? or is there anything wrong?

Your results would indicate simply that while one protein subunit
fluctuates more, the other becomes somewhat more rigid. That's
plausible,
but perhaps not intuitive. Keep in mind that RMSF is very sensitive to
whether or not your simulations are actually converged, and a single
trajectory under each condition is insufficient to make very solid claims
about anything. How long are the simulations? How much of the initial
time is being disregarded, and thus how long are the equilibrated
segments
of the simulations? How different are T1 and T2?

-Justin

--
====

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justinhttp://vt.edu/Pages/Personal/justin
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Re: [gmx-users] Asymmetry in homo dimer simulation

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,

Not using single trajectories. Your job is to convince reviewers that
your work is sound. A single trajectory is not convincing, at least to any
reviewer that does his or her homework :)

-Justin

--
==**==

[gmx-users] Dimer jumping during simulation

2012-12-01 Thread Kavyashree M

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 need to calculate the radius of gyration of dimer, this value differs
when i use treated and untreated trajectories.
So Kindly suggest some solution.

Thank you
kavya
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[gmx-users] Re: Dimer jumping during simulation

2012-12-01 Thread Kavyashree M

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.
 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 need to calculate the radius of gyration of dimer, this value differs
 when i use treated and untreated trajectories.
 So Kindly suggest some solution.

 Thank you
 kavya

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Re: [gmx-users] problem in running md simulation

2012-11-16 Thread Kavyashree M

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, ananyachatterjee 
ananyachatter...@iiserkol.ac.in wrote:

 Hi all,

 As suggested by venhat I have energy minimised it till 1000Kj/mol but even
 now I am getting the same error, saying

 Warning: 1-4 interaction between 3230 and 3233 at distance 3.573 which is
 larger than the 1-4 table size 2.400 nm
 These are ignored for the rest of the simulation
 This usually means your system is exploding,
 if not, you should increase table-extension in your mdp file
 or with user tables increase the table size

 t = 90.674 ps: Water molecule starting at atom 236548 can not be settled.
 Check for bad contacts and/or reduce the timestep.
 Wrote pdb files with previous and current coordinates

 --**-
 Program mdrun, VERSION 4.0.7
 Source code file: ../../../../src/mdlib/nsgrid.**c, line: 348

 Fatal error:
 Number of grid cells is zero. Probably the system and box collapsed.

 can anyone suggest me what to do now.

 Ananya Chatterejee



  On Thu, 15 Nov 2012 11:38:17 +0530, Venkat Reddy wrote:

 I think the system is not well energy minimized. Do it for 1000kj/mol.
 Also
 check for bad contacts in your starting structure using Ramachandran plot.
 One more important thing is that, you have to generate an index file with
 Protein_GTP as one group and water_Ions as another. Then change your
  tc-groups as

 tc-grps = Protein_GTP   Water_Ions
 tau_t   =  0.1 0.1 ; time constant, in ps
 ref_t   =   300   300


 On Thu, Nov 15, 2012 at 10:50 AM, ananyachatterjee 
 ananyachatter...@iiserkol.ac.**in ananyachatter...@iiserkol.ac.in
 wrote:

  Hi all,

 I was running a md simulation of protein complexed with GTP in water,
 neutralised with Mg2+ and Cl- ions.I have also em the system to
 2000kj/mol
 and also equilibrated the water molecules in 300K temperature and 1 bar
 pressure. And then run the md simulation using md parameters as follow:

 title   = Protein-ligand complex
 ; Run parameters
 integrator  = md; leap-frog integrator
 nsteps  = 50   ; 2 * 500 = 1000 ps (1 ns)
 dt  = 0.002 ; 2 fs
 ; Output control
 nstxout = 500  ; save coordinates every 1ps
 nstvout = 500   ; save coordinates every 1ps
 nstenergy   = 500  ; save energies every 1 ps
 nstlog  = 500  ; update log file every 1 ps
 nstxtcout   = 500  ; write .xtc trajectory every 1 ps
 energygrps  = Protein GTP SOL MG2+
 ; Bond parameters
 constraints = none; No constrains
 ; Neighborsearching
 ns_type = grid  ; search neighboring grid cells
 nstlist = 5 ; 10 fs
 rlist   = 0.9   ; short-range neighborlist cutoff (in nm)
 rcoulomb= 0.9   ; short-range electrostatic cutoff (in nm)
 rvdw= 1.4   ; short-range van der Waals cutoff (in nm)
 ; Temperature coupling
 tcoupl  = v-rescale  ; modified Berendsen thermostat
 tc-grps = Protein GTP   SOL  MG2+  CL-; two coupling groups -
 more
 accurate
 tau_t   = 0.1 0.1   0.1  0.1  0.1 ; time constant, in ps
 ref_t   = 300 300   300  300  300; reference temperature, one
 for each group, in K
 ; Pressure coupling
 pcoupl  = Parrinello-Rahman ; pressure coupling is on for
 NPT
 pcoupltype  = isotropic ; uniform scaling of box
 vectors
 tau_p   = 2.0   ; time constant, in ps
 ref_p   = 1.0   ; reference pressure, in bar
 compressibility = 4.5e-5; isothermal compressibility
 of water, bar^-1
 refcoord_scaling= com
 ; Periodic boundary conditions
 pbc = xyz   ; 3-D PBC


 Now I am getting the following error.


 Warning: 1-4 interaction between 3231 and 3234 at distance 10.730 which
 is
 larger than the 1-4 table size 2.400 nm
 These are ignored for the rest of the simulation
 This usually means your system is exploding,
 if not, you should increase table-extension in your mdp file
 or with user tables increase the table size

 t = 226.610 ps: Water molecule starting at atom 236548 can not be
 settled.
 Check for bad contacts and/or reduce the timestep.
 Wrote pdb files with previous and current coordinates

 ---
 Program mdrun, VERSION 4.0.7
 Source code file: ../../../../src/mdlib/nsgrid.c, line: 348

 Fatal error:
 Number of grid cells is zero. Probably the system and box collapsed.

 kindly help me I am not getting where I am getting wrong.



 --
 Ananya Chatterjee,
 Senior Research Fellow (SRF),
 Department of biological Science,
 IISER-Kolkata.
 --
 gmx-users mailing list

Re: [gmx-users] problem in running md simulation

2012-11-16 Thread Kavyashree M

Oh, I am sorry That is right. But its difficult
to find The specific cutoff values to be used
for different protocols of cutoff, switch and shift..
different values are stated in different papers..
And original force field paper (eg OPLSAA) does
not explicitly specify these values.
Any references 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
 interaction decreases as (1/r).. so it would be better if
 you consider columbic interaction for longer distance
 than vdw interaction..


 One should not make haphazard changes to cutoffs.  They are part of the
 force field.  Changing them without basis can invalidate the force field
 model.

 -Justin

  bye
 kavya

 On Fri, Nov 16, 2012 at 8:32 PM, ananyachatterjee 
 ananyachatter...@iiserkol.ac.**in ananyachatter...@iiserkol.ac.in
 wrote:

  Hi all,

 As suggested by venhat I have energy minimised it till 1000Kj/mol but
 even
 now I am getting the same error, saying

 Warning: 1-4 interaction between 3230 and 3233 at distance 3.573 which is
 larger than the 1-4 table size 2.400 nm
 These are ignored for the rest of the simulation
 This usually means your system is exploding,
 if not, you should increase table-extension in your mdp file
 or with user tables increase the table size

 t = 90.674 ps: Water molecule starting at atom 236548 can not be settled.
 Check for bad contacts and/or reduce the timestep.
 Wrote pdb files with previous and current coordinates

 ---
 Program mdrun, VERSION 4.0.7
 Source code file: ../../../../src/mdlib/nsgrid.c, line: 348

 Fatal error:
 Number of grid cells is zero. Probably the system and box collapsed.

 can anyone suggest me what to do now.

 Ananya Chatterejee



   On Thu, 15 Nov 2012 11:38:17 +0530, Venkat Reddy wrote:

  I think the system is not well energy minimized. Do it for 1000kj/mol.
 Also
 check for bad contacts in your starting structure using Ramachandran
 plot.
 One more important thing is that, you have to generate an index file
 with
 Protein_GTP as one group and water_Ions as another. Then change your
   tc-groups as

 tc-grps = Protein_GTP   Water_Ions
 tau_t   =  0.1 0.1 ; time constant, in ps
 ref_t   =   300   300


 On Thu, Nov 15, 2012 at 10:50 AM, ananyachatterjee 
 ananyachatter...@iiserkol.ac.in 
 ananyachatter...@iiserkol.ac.**inananyachatter...@iiserkol.ac.in
 
 wrote:

   Hi all,


 I was running a md simulation of protein complexed with GTP in water,
 neutralised with Mg2+ and Cl- ions.I have also em the system to
 2000kj/mol
 and also equilibrated the water molecules in 300K temperature and 1 bar
 pressure. And then run the md simulation using md parameters as follow:

 title   = Protein-ligand complex
 ; Run parameters
 integrator  = md; leap-frog integrator
 nsteps  = 50   ; 2 * 500 = 1000 ps (1 ns)
 dt  = 0.002 ; 2 fs
 ; Output control
 nstxout = 500  ; save coordinates every 1ps
 nstvout = 500   ; save coordinates every 1ps
 nstenergy   = 500  ; save energies every 1 ps
 nstlog  = 500  ; update log file every 1 ps
 nstxtcout   = 500  ; write .xtc trajectory every 1 ps
 energygrps  = Protein GTP SOL MG2+
 ; Bond parameters
 constraints = none; No constrains
 ; Neighborsearching
 ns_type = grid  ; search neighboring grid cells
 nstlist = 5 ; 10 fs
 rlist   = 0.9   ; short-range neighborlist cutoff (in nm)
 rcoulomb= 0.9   ; short-range electrostatic cutoff (in nm)
 rvdw= 1.4   ; short-range van der Waals cutoff (in nm)
 ; Temperature coupling
 tcoupl  = v-rescale  ; modified Berendsen
 thermostat
 tc-grps = Protein GTP   SOL  MG2+  CL-; two coupling groups -
 more
 accurate
 tau_t   = 0.1 0.1   0.1  0.1  0.1 ; time constant, in ps
 ref_t   = 300 300   300  300  300; reference temperature,
 one
 for each group, in K
 ; Pressure coupling
 pcoupl  = Parrinello-Rahman ; pressure coupling is on
 for
 NPT
 pcoupltype  = isotropic ; uniform scaling of box
 vectors
 tau_p   = 2.0   ; time constant, in ps
 ref_p   = 1.0   ; reference pressure, in
 bar
 compressibility = 4.5e-5; isothermal
 compressibility
 of water, bar^-1
 refcoord_scaling= com
 ; Periodic boundary conditions
 pbc = xyz   ; 3-D PBC


 Now I am getting the following error.


 Warning: 1-4 interaction between 3231 and 3234 at distance 10.730 which
 is
 larger than the 1-4 table size 2.400 nm
 These are ignored for the rest of the simulation
 This usually means your system is exploding

Re: [gmx-users] how to restart a stopped simulation

2012-11-11 Thread Kavyashree M

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 to
 restart it from the same point.
 --
 Ananya Chatterjee,

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Re: [gmx-users] how to check the intermediate coordinated even when the simulation is running

2012-11-09 Thread Kavyashree M

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 violation using g_mindist. Other things
what you have to check depends on the parameter you want to see.

Probably others may give a better answer regarding this.

Bye
kavya

On Fri, Nov 9, 2012 at 5:04 PM, ananyachatterjee
ananyachatter...@iiserkol.ac.in wrote:

I am very new to this MD simulation, by reading the tutorials in the
website I have run an simulation and it is running from last 5 day and I am
not getting whether it is running properly or not. Could any one kindly
tell me how to see whether the simulation is running or not and also how
can I check the intermediate coordinated even when the simulation is
running. Kindly help me.
--
Ananya Chatterjee,

Re: [gmx-users] g_saltbr speed

2012-07-13 Thread Kavyashree M

Dear users,

Its the continuation of the question I asked yesterday, Inorder to reduce
the memory usage during g_saltbr calculations i got the trajectory of only
protein, and tpr file without water and was able to successfully run it. But
unfortunately this again got stopped at 36ns as it had 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 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 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?


 In principle, you should be prompted to choose a default group, but you can
 also use a custom index group as needed.

 The warning message is intended to note that the .tpr file you produce will
 not likely work for running an actual simulation.  It should be fine for
 analysis.


 -Justin

 --
 

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 


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Re: [gmx-users] g_saltbr speed

2012-07-13 Thread Kavyashree M

Its 50ns 25000 frames. the xtc file is 695MB. it has 16GB RAM. So will
that be insufficient? I have previously run other analysis which used to take
huge memory, for eg. covariance analysis, in a system with much lesser memory
even though CPU usage was low the job used to finish. But in this case 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 the trajectory of only
 protein, and tpr file without water and was able to successfully run it.
 But
 unfortunately this again got stopped at 36ns as it had 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.


 How long is the trajectory?  How many frames?  What is the size of the file
 on disk?  It sounds to me like you're simply exhausting available memory, so
 the only advice is in the link I posted before - use fewer frames or use a
 machine that has more memory to do the analysis.


 -Justin

 --
 

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 


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Re: [gmx-users] g_saltbr speed

2012-07-13 Thread Kavyashree M

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 which used to
 take
 huge memory, for eg. covariance analysis, in a system with much lesser
 memory
 even though CPU usage was low the job used to finish. But in this case its
 not
 so.


 I can't see a reason why the file itself would present a problem.  I have
 run g_saltbr on similarly sized systems.  Sorry, I can't offer an
 explanation as to why it's stopping prematurely.


 -Justin

 --
 

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 


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[gmx-users] g_saltbr speed

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 @ 3.40GHz
where i ran MD. Please give some suggestion as to how to
increase the speed of calculation.
Command i issued was:
g_saltbr -f ../traj.xtc -s md.tpr -t 0.4 -sep

Thank you
Kavya
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Re: [gmx-users] g_saltbr speed

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% since long and CPU usage drops down to 1.5 -2 %
but in many cases i have seen that still it will run (off course
slowly) and finish. But this was too long. So any 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 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 @ 3.40GHz
 where i ran MD. Please give some suggestion as to how to
 increase the speed of calculation.
 Command i issued was:
 g_saltbr -f ../traj.xtc -s md.tpr -t 0.4 -sep


 g_saltbr calculates properties of all possible ionic pairs in the system, so
 if there are many, the calculation might take a long time.  Four days sounds
 ridiculous, and perhaps the program has frozen by exhausting the available
 memory.

 -Justin

 --
 

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 


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Re: [gmx-users] g_saltbr speed

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% since long and CPU usage drops down to 1.5 -2 %
 but in many cases i have seen that still it will run (off course
 slowly) and finish. But this was too long. So any suggestions?


 http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume


 -Justin

 --
 

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 


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Re: [gmx-users] g_saltbr speed

Dear Sir,

I had a problem again during g_saltbr calculation it needs
.xtc and .tpr file, I can reduce the .xtc file to have only
protein but .tpr file will have water also in it. inorder to generate
new tpr file without water using grompp, i need topology file
without water .. so do you suggest 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 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% since long and CPU usage drops down to 1.5 -2 %
 but in many cases i have seen that still it will run (off course
 slowly) and finish. But this was too long. So any suggestions?


 http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume


 -Justin

 --
 

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 


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Re: [gmx-users] g_saltbr speed

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 it needs
 .xtc and .tpr file, I can reduce the .xtc file to have only
 protein but .tpr file will have water also in it. inorder to generate
 new tpr file without water using grompp, i need topology file
 without water .. so do you suggest me to go this way.. it
 appears quite complicated!


 In fact, it's quite easy with tpbconv.  From tpbconv -h:

 3. by creating a .tpx file for a subset of your original tpx file, which is
 useful when you want to remove the solvent from your .tpx file, or when you
 want to make e.g. a pure Calpha .tpx file. Note that you may need to use
 -nsteps -1 (or similar) to get this to work. WARNING: this .tpx file is not
 fully functional.


 -Justin

 --
 

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 


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Re: [gmx-users] g_saltbr speed

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 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 it needs
 .xtc and .tpr file, I can reduce the .xtc file to have only
 protein but .tpr file will have water also in it. inorder to generate
 new tpr file without water using grompp, i need topology file
 without water .. so do you suggest me to go this way.. it
 appears quite complicated!


 In fact, it's quite easy with tpbconv.  From tpbconv -h:

 3. by creating a .tpx file for a subset of your original tpx file, which is
 useful when you want to remove the solvent from your .tpx file, or when you
 want to make e.g. a pure Calpha .tpx file. Note that you may need to use
 -nsteps -1 (or similar) to get this to work. WARNING: this .tpx file is not
 fully functional.


 -Justin

 --
 

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 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 


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Re: [gmx-users] g_saltbr speed

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 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?


 In principle, you should be prompted to choose a default group, but you can
 also use a custom index group as needed.

 The warning message is intended to note that the .tpr file you produce will
 not likely work for running an actual simulation.  It should be fine for
 analysis.


 -Justin

 --
 

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540) 231-9080
 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

 


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[gmx-users] homodimer simulation

2012-01-10 Thread Kavyashree M

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 different from each other in few
regions. I was expecting similar rmsf for both the monomers.
I checked the pdb file generated after md run, it did not have chain
ID but two chains were present.

Kindly let me know what is wrong with rmsf? Or what is wrong with
simulation.

Thanking you
With Regards
avya
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[gmx-users] Number of nodes

2011-10-31 Thread Kavyashree M

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 machines. Kindly
suggest the possible solutions.

Thanking you
With Regards
Kavya
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Re: [gmx-users] Number of nodes

2011-10-31 Thread Kavyashree M

Hello,

System Admin said that the Job fails on 32 and 128 because memory
is insufficient for each task, so upon increasing the nodes, data gets
distributed across more number of nodes and each node gets less
memory occupancy and he also mentioned that he was able to run
on 512 nodes 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)
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.

Sounds like your system admin should be offering you some more help, since
they know the specifics of the hardware, queuing software, etc.

I am not familiar with the bluegene machines. Kindly
suggest the possible solutions.

Without seeing your input file(s), there's nothing anyone can do. Be
mindful that this list pertains to Gromacs-specific problems, which do not
seem to be present here.

-Justin

--
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Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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Re: [gmx-users] High temperature Simulation

2011-10-18 Thread Kavyashree M

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 difficult to simulate at high pressure due to
stability reasons.)

Thank you
With Regards
Kavya
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Re: [gmx-users] High temperature Simulation

2011-10-18 Thread Kavyashree M

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 exactly it will
eliminate the boiling issue if we dont use higher
pressure while equlibrating? (as you said that
it is difficult to simulate at high pressure due to
stability reasons.)

You should equilibrate under whatever the necessary conditions are, be it
high pressure or not. Once the desired parameters have been achieved, then
switch to NVT. Since the box is invariant in NVT, you don't have to worry
about anything expanding.

Please continue to search in the literature for finer methodology points.
I'm certain these issues have been addressed in greater detail elsewhere.

-Justin

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[gmx-users] High temperature Simulation

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 simulate an unfolding event)
I have a reference -
Biophysical Journal Volume 94 June 2008 –4453

Any other references or suggestions will be helpful.

Thanking you
With Regards
M. Kavyashree
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Re: [gmx-users] High temperature Simulation

Thank you,

What about the pressure that need to be used at that temperature
(for a system of a protein in tip4p water)

Thank you
With Regards
Kavya

On Mon, Oct 17, 2011 at 3:29 PM, bipin singh bipinel...@gmail.com wrote:

 As far as I know we do energy minimization at room temperature only.
 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 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 simulate an unfolding event)
  I have a reference -
  Biophysical Journal Volume 94 June 2008 –4453
 
  Any other references or suggestions will be helpful.
 
  Thanking you
  With Regards
  M. Kavyashree
 
 
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Re: [gmx-users] High temperature Simulation

Hello,

The set pressure should reflect whatever system you are trying to model.

This statement is not very clear to me.. But when the mdout.mdp file after
grompp
during energy minimization is examined it says -

gen-vel = no
gen-temp = 300
gen-seed = 173529

Even though I have not assigned any velocities in em.mdp file. Thats the
reason why got this doubt about temperature during energy minimization.

Thank you
With Regards
Kavya

-Justin

Thank you
With Regards
Kavya

On Mon, Oct 17, 2011 at 3:29 PM, bipin singh bipinel...@gmail.commailto:
bipinel...@gmail.com wrote:

As far as I know we do energy minimization at room temperature only.
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
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 the energy minimization step also needs to be done at high
temperature? (here my aim is not to simulate an unfolding event)
I have a reference -
Biophysical Journal Volume 94 June 2008 –4453

Any other references or suggestions will be helpful.

Thanking you
With Regards
M. Kavyashree

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Re: [gmx-users] High temperature Simulation