[gmx-users] MD Simulations

[pawan raghav]

Dear friends,

Please read nice article on MD Simulations

http://www.springerlink.com/content/6jt0843463226321/

-- 
Pawan
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[gmx-users] Please rectify free energy problem

[pawan raghav]

g_lie calculates the deltaG= alpha(Vl-s LJp - Vl-s LJw) + beta(Vl-s
elp - Vl-s elw) equation. But when calculating DGbind from g_lie it will
ask for only one term at a time i.e. -Elj for either Vl-s LJp or Vl-s
LJw and -Eqq for either Vl-s elp  or Vl-s elw. My question is when
using only Vl-s LJp for -Elj and Vl-s elp for  -Eqq, how the LJ and EL
terms calculated for ligand-water interaction or in vice-versa condition for
ligand-protein interactions to complete the deltaG equation?

-- 
Pawan
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[gmx-users] g_lie

[pawan raghav]

g_lie calculates the deltaG= alpha(Vl-s LJp - Vl-s LJw) + beta(Vl-s
elp - Vl-s elw) equation. But when calculating DGbind from g_lie it will
ask for only one term at a time i.e. -Elj for either Vl-s LJp or Vl-s
LJw and -Cqq for either Vl-s elp  or Vl-s elw. My question is when
using only Vl-s LJp for -Elj and Vl-s elp for  -Cqq, how the LJ and EL
terms calculated for ligand-water interaction or in vice-versa condition for
ligand-protein interactions to complete the deltaG equation?

-- 
Pawan
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[gmx-users] Free energy

[pawan raghav]

g_lie calculates the deltaG= alpha(Vl-s LJp - Vl-s LJw) + beta(Vl-s
elp - Vl-s elw) equation. But when calculating DGbind from g_lie it will
ask for only one term at a time i.e. -Elj for either Vl-s LJp or Vl-s
LJw and -Cqq for either Vl-s elp  or Vl-s elw. My question is when
using only Vl-s LJp for -Elj and Vl-s elp for  -Cqq, how the LJ and EL
terms calculated for ligand-water interaction or in vice-versa condition for
ligand-protein interactions to complete the deltaG equation?

-- 
Pawan
-- 
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[gmx-users] Installation error

[pawan raghav]

I have already posted this error report on 6 Dec 2010 but still have not
getting any solution. So I am thankful if any one can rectify the solution
of installation problem i.e. While installing gromacs-4.5.3 I got an error
on executing make command. I am installing this gromacs version on cygwin.
The error written below, please tell me solution of this error.

Creating library file: .libs/libgmx.dll.a

.libs/checkpoint.o:checkpoint.c:(.text+0xcd): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x13c): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x236): undefined reference to
`_xdr_double'

.libs/checkpoint.o:checkpoint.c:(.text+0x256): undefined reference to
`_xdr_vector'

.libs/checkpoint.o:checkpoint.c:(.text+0x3f0): undefined reference to
`_xdr_float'

.libs/checkpoint.o:checkpoint.c:(.text+0x408): undefined reference to
`_xdr_vector'

.libs/checkpoint.o:checkpoint.c:(.text+0x64e): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0xfad): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0xff0): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x10a3): undefined reference to
`_xdr_double'

.libs/checkpoint.o:checkpoint.c:(.text+0x10bb): undefined reference to
`_xdr_vector'

.libs/checkpoint.o:checkpoint.c:(.text+0x127d): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x12c0): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x1372): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x138a): undefined reference to
`_xdr_vector'

.libs/checkpoint.o:checkpoint.c:(.text+0x1fb9): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x24cf): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x256a): undefined reference to
`_xdr_string'

.libs/checkpoint.o:checkpoint.c:(.text+0x2606): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x2642): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x26d4): undefined reference to
`_xdr_string'

.libs/checkpoint.o:checkpoint.c:(.text+0x2755): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x2791): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x27de): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x283a): undefined reference to
`_xdr_u_char'

.libs/checkpoint.o:checkpoint.c:(.text+0x287a): undefined reference to
`_xdr_u_char'

.libs/checkpoint.o:checkpoint.c:(.text+0x28ba): undefined reference to
`_xdr_u_char'

.libs/checkpoint.o:checkpoint.c:(.text+0x28fa): undefined reference to
`_xdr_u_char'

.libs/checkpoint.o:checkpoint.c:(.text+0x293a): undefined reference to
`_xdr_u_char'

.libs/checkpoint.o:checkpoint.c:(.text+0x297a): more undefined references to
`_xdr_u_char' follow

.libs/checkpoint.o:checkpoint.c:(.text+0x2f00): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x2f8e): undefined reference to
`_xdr_string'

.libs/checkpoint.o:checkpoint.c:(.text+0x2ffc): undefined reference to
`_xdr_string'

.libs/checkpoint.o:checkpoint.c:(.text+0x3070): undefined reference to
`_xdr_string'

.libs/checkpoint.o:checkpoint.c:(.text+0x30e4): undefined reference to
`_xdr_string'

.libs/checkpoint.o:checkpoint.c:(.text+0x3158): undefined reference to
`_xdr_string'

.libs/checkpoint.o:checkpoint.c:(.text+0x31cc): more undefined references to
`_xdr_string' follow

.libs/checkpoint.o:checkpoint.c:(.text+0x3236): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x328f): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x32d3): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x334a): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x3412): undefined reference to
`_xdr_double'

.libs/checkpoint.o:checkpoint.c:(.text+0x3457): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x34b1): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x3501): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x3551): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x358e): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x35d2): more undefined references to
`_xdr_int' follow

.libs/checkpoint.o:checkpoint.c:(.text+0x392f): undefined reference to
`_xdr_string'

.libs/checkpoint.o:checkpoint.c:(.text+0x3a31): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x3a75): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x4cb4): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x5216): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x6c90): undefined reference to
`_xdr_int'

[gmx-users] Extreme

[pawan raghav]

Dear tsjerk,

I am very sorry to say that your suggestions does not help but increase
confusions only. I am highly obliged if you give me clear statements about
the scores to understand this concept in depth. I have searched research
article about this concept but failed to find even an single article.
Neither Gromacs tutorial give any description about these scores, nor your
PCA tutorial. I am really interested to understand this concept so help by
giving me answers of my questions.

eigenvector   Minimum   Maximum

 value   time  value   time

  1  -9.162661   99.0   2.682097 9450.0

  2  -2.728093 4695.0   3.272116  558.0


I got clearcut idea about this line after read your tutorial *These are the
maximum and minimum projections on the eigenvectors.*

What is the meaning of this line here? *They are very unlikely to
correspond to energy minima, as minima will be modal.*

If the values in second column not the energy values they are scores only.*
*Are scores directly corresponds to the energy minima for second column and
energy maxima for 4th column on which they are based? I have seen that in
second column there are negative values (Minimum) and in 4th column there
are positive values (Maximum). In above example along the first eigenvector,
Are -9.162661 value at time 99 ps corresponding to the structure at low
energy during the projection and the value 2.682097 score corresponds to the
maximum energy. If I am wrong then tell me, what are the criteria on which
there scores are based?

I am totally agree with your this concept and understand completely in this
line *Think of a pendulum, projecting the position on the floor.*

But this statement confused me *The extreme projections actually correspond
to states of higher (potential) energy*. Which extreme projection
corresponds to state of higher (potential) energy either minimum or maximum
or both of them?

Please reply me line by line so that I can understand this concept.

-- 
Pawan Kumar Raghav
Bioinformatician
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[gmx-users] Extreme

[pawan raghav]

Dear Justin,

Thanks for sharing your knowledge with me. I have gone through the tutorial
and observed -extrn extract projected structure along with
first two eigen vectors. Each Eigen Vector represents minimum and maximum
strucuture value.

I am a bit confiused about the values for minimum and maximum. I dont know
the exact meaning of score for minmum and maximum values. Are these values
 deviation (Displacement) and what is its unit and which score is the best
score along any eigen vector?

Please help me out with this problem. Is it possible to extract minimum
energy sructructue from a MD trajectory by using G_anaeig. Give me some clue
about these minimum/maximum scores.Can i consider thhis mimimum or maximum
structure as a native structure?

Pawan Raghav
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[gmx-users] g_anaeig

[pawan raghav]

I am postin ths question second time so please solve this issue
g_anaeig generated numbers of c-alpha or protein structures through -extr
extreme.pdb. The bash shell show numbers of eigenvector structures starting
from first to last frames are as follows

eigenvector   Minimum   Maximum

value   time  value   time

 1   4.88046714148.0   7.74721812501.0

 2   1.63742113926.0   4.34406313110.0

 3  -0.07439312567.0   2.74582614166.0

 4   0.94024012618.0   5.18128314265.0

 5  -2.76056614760.0  -0.10756412789.0

 6   0.39418412627.0   2.69352014997.0

First column shows vectors, but what are the values in second column? Are
they represents energy values in kJ/mol in second and fourth column?

-- 
Pawan
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[gmx-users] g_anaeig

[pawan raghav]

Dear justin,

Thanks for your useful suggestions but not the right way to post these
things. Anyway Dear I have already read the link mentioned by you and know
very well what does -extr do actually I want to extract some minimum energy
structure for docking studies from 12500 ps to 15000 ps MD trajectory out of
total 15 ns MD run. For this, I have extract structures along 50
eigenvectors structures. Therefore, I want to confirm the values in second
column whether they are energy values or not.

-- 
Pawan
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[gmx-users] anaeig

[pawan raghav]

g_anaeig generated numbers of c-alpha or protein structures through -extr
extreme.pdb. The bash shell show numbers of eigenvector structures starting
from first to last frames are as follows

eigenvector   Minimum   Maximum

 value   time  value   time

  1   4.88046714148.0   7.74721812501.0

  2   1.63742113926.0   4.34406313110.0

  3  -0.07439312567.0   2.74582614166.0

  4   0.94024012618.0   5.18128314265.0

  5  -2.76056614760.0  -0.10756412789.0

  6   0.39418412627.0   2.69352014997.0

First column shows vectors, but what are the values in second column? Are
they represents energy values in kJ/mol in second and fourth column?

-- 
Pawan
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[gmx-users] gromacs-4.5.3 installation error

[pawan raghav]

Dear users,

While installing gromacs-4.5.3 I got an error on executing make command. I
am installing this gromacs version on cygwin. The error written below,
please tell me about the error  where I was wrong

Creating library file: .libs/libgmx.dll.a

.libs/checkpoint.o:checkpoint.c:(.text+0xcd): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x13c): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x236): undefined reference to
`_xdr_double'

.libs/checkpoint.o:checkpoint.c:(.text+0x256): undefined reference to
`_xdr_vector'

.libs/checkpoint.o:checkpoint.c:(.text+0x3f0): undefined reference to
`_xdr_float'

.libs/checkpoint.o:checkpoint.c:(.text+0x408): undefined reference to
`_xdr_vector'

.libs/checkpoint.o:checkpoint.c:(.text+0x64e): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0xfad): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0xff0): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x10a3): undefined reference to
`_xdr_double'

.libs/checkpoint.o:checkpoint.c:(.text+0x10bb): undefined reference to
`_xdr_vector'

.libs/checkpoint.o:checkpoint.c:(.text+0x127d): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x12c0): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x1372): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x138a): undefined reference to
`_xdr_vector'

.libs/checkpoint.o:checkpoint.c:(.text+0x1fb9): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x24cf): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x256a): undefined reference to
`_xdr_string'

.libs/checkpoint.o:checkpoint.c:(.text+0x2606): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x2642): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x26d4): undefined reference to
`_xdr_string'

.libs/checkpoint.o:checkpoint.c:(.text+0x2755): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x2791): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x27de): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x283a): undefined reference to
`_xdr_u_char'

.libs/checkpoint.o:checkpoint.c:(.text+0x287a): undefined reference to
`_xdr_u_char'

.libs/checkpoint.o:checkpoint.c:(.text+0x28ba): undefined reference to
`_xdr_u_char'

.libs/checkpoint.o:checkpoint.c:(.text+0x28fa): undefined reference to
`_xdr_u_char'

.libs/checkpoint.o:checkpoint.c:(.text+0x293a): undefined reference to
`_xdr_u_char'

.libs/checkpoint.o:checkpoint.c:(.text+0x297a): more undefined references to
`_xdr_u_char' follow

.libs/checkpoint.o:checkpoint.c:(.text+0x2f00): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x2f8e): undefined reference to
`_xdr_string'

.libs/checkpoint.o:checkpoint.c:(.text+0x2ffc): undefined reference to
`_xdr_string'

.libs/checkpoint.o:checkpoint.c:(.text+0x3070): undefined reference to
`_xdr_string'

.libs/checkpoint.o:checkpoint.c:(.text+0x30e4): undefined reference to
`_xdr_string'

.libs/checkpoint.o:checkpoint.c:(.text+0x3158): undefined reference to
`_xdr_string'

.libs/checkpoint.o:checkpoint.c:(.text+0x31cc): more undefined references to
`_xdr_string' follow

.libs/checkpoint.o:checkpoint.c:(.text+0x3236): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x328f): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x32d3): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x334a): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x3412): undefined reference to
`_xdr_double'

.libs/checkpoint.o:checkpoint.c:(.text+0x3457): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x34b1): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x3501): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x3551): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x358e): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x35d2): more undefined references to
`_xdr_int' follow

.libs/checkpoint.o:checkpoint.c:(.text+0x392f): undefined reference to
`_xdr_string'

.libs/checkpoint.o:checkpoint.c:(.text+0x3a31): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x3a75): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x4cb4): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x5216): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x6c90): undefined reference to
`_xdr_int'

.libs/checkpoint.o:checkpoint.c:(.text+0x76ca): more undefined references to
`_xdr_int' follow

.libs/enxio.o:enxio.c:(.text+0xc72): undefined reference to 

[gmx-users] PR

[pawan raghav]

I have read that SPC/SPCE is an rigid and pre-equilibrated 3 point water
model. Is it likely mean that position restrained dynamics is not required.
If we are not intersted in position restrained dynamics then what are the
criteria for system needed.

-- 
Pawan
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[gmx-users] PR

[pawan raghav]

Thank mark for comments, but I have check the structure after energy
minimization through ramachandran plot and found 82% residues were lies in
core region. After performed position restrained dynamics it reduced to 52%
in core region also 1 bad contact was found. I have taken SPC water model
then add 2 NA+ ions in the solvent, done energy minimization at emtol value
of 2000 kJ/mol and steps for 250. Below is the pr.mdp file for position
restraiuned dynamics, please let me know if any serious flaws. So help me by
giving me the reference.

title = Position restrained of Bcl-2.

integrator = md

define = -DPOSRES

dt = 0.002

nsteps = 10

nstcomm = 1

nstxout = 250

nstvout = 1000

nstfout = 0

nstlog = 10

nstenergy = 10

nstlist = 5

xtc_grps = protein sol

energygrps = protein sol

ns_type = grid

rlist = 1.0

coulombtype = PME

rcoulomb = 1.0

vdwtype = cut-off

rvdw = 1.4

fourierspacing = 0.135

fourier_nx = 0

fourier_ny = 0

fourier_nz = 0

pme_order = 4

ewald_rtol = 1e-5

optimize_fft = yes

Dispcorr = no

Tcoupl = v-rescale

tc-grps = protein sol NA+

tau_t = 0.1 0.1 0.1

ref_t = 300 300 300

Pcoupl = parrinello-rahman

Pcoupltype = isotropic

tau_p = 0.5

compressibility = 4.5e-5

ref_p = 1.0

gen_vel = yes

gen_temp = 300.0

gen_seed = 173529

constraints = all-bonds


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[gmx-users] Position restrained..

[pawan raghav]

Dear All,

Hope this mail will find you in good health.

I am facing a problem regarding Position restrained dynamics (PR). I have
done Molecular dynamic simulation
(for cytosolic protein) but has not performed PR. So i m little confused if
this effects the results and if yes to what extent it effects the outcome,

Earlier, i performed PR as it is recomended but in my cases ,the generated
structure was not correct as the core residues found to be
reduced from 82%-52% and one bad contact was also observed. So i skipped the
PR Step and run MD
simultaion just after energy Minimization.

I was wondering if PR is always necessary before molecular simulation
without any exception. And if not, how can i justify this protocol
that we have performed without PR. Or where i can find the references to
justify the my protocol.

Pawan Kumar Raghav
Bioinformatician
Stem Cell and Gene Therapy Research Group
Division of Radiation Biosciences
INMAS, DRDO
Timarpur Delhi-110054

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Stem Cell and Gene Therapy Research Group
Division of Radiation Biosciences
INMAS, DRDO
Timarpur Delhi-110054
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[gmx-users] Area per atom

[pawan raghav]

Dear All

Using g_sas on trajectory file with command

g_sas -f .xtc -s .tpr -oa atomarea.xvg

gives following output

@title Area per atom

@xaxis  label Atom #

@yaxis  label Area (nm\S2\N)

@TYPE xy

1 0.139885 0.0351154

2 0.0510893 0.0236223

3 0.0510077 0.0234374

4 0.0512037 0.0234554

5 0.0284763 0.0401088

6 0.236609 0.108979

The first column is atom no. and what are the values in second column.

I have found this question reply i.e.
Ans: Average area per atom, then some sort of fluctuation term.

So please tell me, what is the meaning of some sort of fluctuation term as
shown in red colour in graph?

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[gmx-users] contact residues

[pawan raghav]

I have used g_mdmat
g_mdmat -f traj.xtc -s md.tpr -mean dm.xpm -frames dmf.xpm -no num.xvg

I got dm.xpm graph which shows mean of whole simulation residue contacts.
How to get information about the particular residue are in contact? how to
get list of contact residues?

In graph file num.xvg there are three columns which I am not able to
understand i.e. total, mean and natm. What is total, mean and natom

Please rectify this

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[gmx-users] minima

[pawan raghav]

g_anaeig command give some minimum or maximum value are these value
energy minima and maxima for extreme 2 frame structures?
eigenvector   Minimum   Maximum

 value   time  value   time

  1  -9.162661   99.0   2.682097 9450.0

  2  -2.728093 4695.0   3.272116  558.0

  3  -3.948283   90.0   3.079716 1194.0

  4  -1.944027 1137.0   2.509744 2466.0

  5  -1.739774 1077.0   2.5609176.0

  6  -2.003240  531.0   2.337445   45.0

  7  -1.538053  870.0   1.749108   42.0

  8  -1.554790  525.0   1.518729 2748.0

  9  -1.31231611364.0   1.124524  825.0

 10  -1.1707780.0   1.345256  345.0



Writing 2 frames along eigenvector 1 to extreme1-101.pdb

Writing 2 frames along eigenvector 2 to extreme1-102.pdb

Writing 2 frames along eigenvector 3 to extreme1-103.pdb

Writing 2 frames along eigenvector 4 to extreme1-104.pdb

Writing 2 frames along eigenvector 5 to extreme1-105.pdb

Writing 2 frames along eigenvector 6 to extreme1-106.pdb

Writing 2 frames along eigenvector 7 to extreme1-107.pdb

Writing 2 frames along eigenvector 8 to extreme1-108.pdb

Writing 2 frames along eigenvector 9 to extreme1-109.pdb

Writing 2 frames along eigenvector 10 to extreme1-1010.pdb






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[gmx-users] g_mdmat

[pawan raghav]

Dear friends,

I have used g_mdmat

g_mdmat -f traj.xtc -s md.tpr -mean dm.xpm -frames dmf.xpm -no num.xvg
I got dm.xpm graph which shows mean of whole simulation residue
contacts. How to get information about the particular residue are n contact?
I mean to say, Is there any tool to give list of contact residue?

In graph file num.xvg there are three columns which I am not able to
understand i.e. total, mean and natm.
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[gmx-users] g_hbond

[pawan raghav]

 Below is the hbond.xvg content 1 coloumn is for time second for numbers,
but I am not getting for 3rd one i.e. Pairs within 0.35 nm is this shows
area in cutoff range?

@ title Hydrogen Bonds

@ xaxis label Time

@ yaxis label Number

@TYPE xy

@ view 0.15, 0.15, 0.75, 0.85

@ legend on

@ legend box on

@ legend loctype view

@ legend 0.78, 0.8

@ legend length 2

@ s0 legend Hydrogen bonds

@ s1 legend Pairs within 0.35 nm

0 2 175

3 2 188

6 3 190

9 4 190

12 2 190

15 3 182

18 0 183

21 3 179


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[gmx-users] g_analyze

[pawan raghav]

In manual g_analyze reads an ascii file and analyzes data sets, in which
input file was graph.xvg. To generate eigenvector and eigenvalue file I have
used g_covar and analyzed eigenvectors by g_aneig. So according to manual
input file should be an ascii file, is it covar.dat file generated by
g_covar. But in actual it needs some graph.xvg file, which file is this .xvg
file should be taken for input.

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[gmx-users] essential dynamics

[pawan raghav]

Hi all,

I have a confusion regarding Essential Dynamics. I have read so many
papers regarding PCA and ED most of the papers among them explained
eigenvectors and eigenvalues are as follows:

if a protein has 207 C alpha residues then the total no of eigenvectors are
3N X 3N, where N= no. of atoms i.e. 3 X 207 = 621 eigenvectors. is it means
that an eigenvector represents an C-alpha residue?

But manual described that representations the direction of motions.

But 3N X 3N is a covariance matrix that means this represents 621 X 621
eigenvectors is it true?

Then when we plot a 2dproj.xvg file between eigenvector 1 and eigenvector 2,
is it mean to plot a 2d graph between first two C-alpha atoms or first two
structures?

Please clearify me where I was wrong.

The 2d graph shows oval and random large trajectory graph which represents
the independent and dependent motion, may I know what does it mean?


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[gmx-users] Essential Dynamics

[pawan raghav]

Dear Tsjerk,

It will be helpful to me if you would like to solve my problem I have
already read your tutorial and so many papers but I am really confused and
thats why mail to you. So please answer me which will help me lot to
understand right concept.

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[gmx-users] Re: PCA

[pawan raghav]

On 8/14/10, pawan raghav pwnr...@gmail.com wrote:

 I have done PCA using first g_covar and got eigval.xvg and eigenvec.trr
 files. The eigenvectors were analyzed by g_anaeig program and got
 eigcomp.xvg, eigrmsf.xvg, proj.xvg, and 2dproj.xvg files. Then I want to
 know
 1. Which file among these shows relative positional fluctuation with
 eigenvector index.
 2. Probability distributions for the displacements along several
 eigenvectors.
 3. Absolute values of the projections of the (normalized) extracted
 vectors.
 4. Cumulative percentage of the motion  of a protein from eigvalues.xvg
 file

 --
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[gmx-users] PCA

[pawan raghav]

I have done PCA using first g_covar and got eigval.xvg and eigenvec.trr
files. The eigenvectors were analyzed by g_anaeig program and got
eigcomp.xvg, eigrmsf.xvg, proj.xvg, and 2dproj.xvg files. Then I want to
know
1. Which file among these shows relative positional fluctuation with
eigenvector index.
2. Probability distributions for the displacements along several
eigenvectors.
3. Absolute values of the projections of the (normalized) extracted vectors.
4. Cumulative percentage of the motion  of a protein from eigvalues.xvg file


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[gmx-users] PCA

[pawan raghav]

I have done PCA using first g_covar and got eigval.xvg and eigenvec.trr
files. The eigenvectors were analyzed by g_anaeig program and got
eigcomp.xvg, eigrmsf.xvg, proj.xvg, and 2dproj.xvg files. Then I want to
know
1. Which file among these shows relative positional fluctuation with
eigenvector index.
2. Probability distributions for the displacements along several
eigenvectors.
3. Absolute values of the projections of the (normalized) extracted vectors.
4. Cumulative percentage of the motion  of a protein from eigvalues.xvg file

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[gmx-users] Averege structure

[pawan raghav]

I have done 15ns MD simulations at 300k temp for a protein finally obtained
an average structure from g_rmsf. so please tell me is output average
structure is a sampled structure? is there no need of remd or sampling
further because I got plateau in RMSD calculation at last?

I have strongly energy minimize by first steepest second by conjugate
gradient of my protein after simulation was completed. I have got 81%
residues in core region of RC plot by using this energy minimization method.
I have also used SPDBv instead of former one method for EM but got 91% core
region residues. Which methods should I choose to get the good model? what
are the essential criteria for a good model?



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[gmx-users] Technical

[pawan raghav]

Dear Justin,

Thanks for the wonderful suggestions which is very clear and informative but
I am confused about some points below

1. Actually my protein is human mitochondrial protein so I have used GROMOS
96 53a6 ff. is it correct? but you have mentioned about the condition
applied, so I don't understand this point because I have a normal protein
which bind on the mitochondrial membrane. So according to you which
conditions should i applied? which preferences you are talking about? Due to
have limited configuration of our hardware we are using core2duo single
processor with 4 GB RAM. So dear please suggest me the concise requirements
for this simulation.

2. My protein does not depend on the temperature that means it is not
thermophilic or mesophilic protein. So for large simulations is it correct
to apply REMD technique. I think that ED sampling should be best but don't
know which should be taken for reference structure. I have tell you about my
system and protein so please suggest me the sampling technique is effective
in my protein case.

3. I know about the energy conservation but don't know about the simulation
stability. So please also tell me is PCA should be performed for simulation
stability or something else analysis should be performed.

4. Why 4-5 fs is more effecient than 3fs?


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[gmx-users] REMD

[pawan raghav]

Dear Justin,

No dear I have not modelled the membrane, my protein is a simple protein
which contained a loop about 59 amino acids. So I am intrested to model this
loop through MD simulation. In this concerned I did 15 ns simulations, but
right now don't know how to perform sampling for my protein (which is not a
membrane, thermophilic or mesophilic protein) on same temperature i.e. 300k.
In this regard is it correct to perform REMD, if yes then tell me how to
perform it on single CPU? I am asking from you again to sure I can perform
ot is it right to use REMD in my protein condition which in not a
thermophilic protein. I think that REMD can only apply to those proteins
which are thermophilic or mesophilic. please comment on this.


Yes I wanted to sample loop dynamics, for which you have mentioned to run
several simulations at the relevant (physiological?) temperature. Is it mean
to run several (2,3,4..etc) diferent simulations at different time steps
like 10ns, 15ns, 20ns, 30 ns etc. and analyze those results to obtain some
averages from each and every simulations but it gives several averages
values then how to sample all these simulations and finally how to get the
average from these simulations.

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[gmx-users] REMD

[pawan raghav]

Dear Justin,

I have read manual there was an equation where T1 and T2 are the two
temperatrure will be assign but in my case I don't have different
temperature. I have to simulate at same temperature.

Is there any other alternative to perform sampling rather than REMD. I am
working on one processor so kindly suggest me the best for sampling.

The force field which I have used was taken reference from paper. so please
inform me if any thing wrong.

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[gmx-users] General Question

[pawan raghav]

Dear GROMACS team members,

I have a general question about the GROMACS, actually I have used GROMACS
for the simulation of 59 amino acids domain part of the protein
containing within it. This domain lies in the position from 34-92 out of 239
residues, this loop having only 12 residues similarity whose does not found
any similarity in this region. I have an objective to predict the behaviour
of such a large loop flexibility. So my question is that at what level of
accuracy, the loop optimization and prediction would be correct. Is it
possible to predict the loop structure on the basis of simulation or can
predict the structure of unstructure loop of a protein? Please comment on
this because some people criticising MD simulations prediction. Can we
predict the folded loop of a protein by using simulation? if yes then tell
me about the analysis methods in gromacs for loop particularly. One more
question is about the dt that it can be possible to change the value of dt
in .mdp file instead of 0.002 ps to 0.003 if yes then what is the
significance of this and what is the efeect of this on simulation?
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[gmx-users] g_covar

[pawan raghav]

Thanks Mark for your advice

Note: The fit analysis group are identical, while the fit is mass weighted
and the analysis is not making the fit non mass weighted.

But, this is the the real unning out put of the command prompt

Please let me know anyone what is the meaning of this note? and also tell me
is it right to choose C-alpha group for two times?   

Yes I want to do the structure-fitting on the same set of atoms as I do the
analysis.

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[gmx-users] PCA

[pawan raghav]

I have a little concept problem regarding principal component analysis. So
my question is about ED sampling are as follows:

1. I have read from the manual that g_covar calculates and diagonalize the
(mass-weighted) covariance matrix. So what is the meaning of mass-weighted
in covariance matrix?

2. g_covar output the eigenval.xvg and and eigenvec.trr, but when I opened
the eigenval.xvg file it will shows nothing, i don't know what was wrong
with it?

3. what is the difference between covariance matrix and normal mode analysis
because both were used to generate the eigenval.xvg and eigenvec.trr file?

4. g_anaeig analyze the eigenvectors, so it is possible to fitted all the
structures generated at the time of simulations of single structure without
using the other structure?

I mean to say that it is possible to use single structure as initial to
simulate and ED sampling?

5. what is the need of eigenvec2.trr input file in g_anaeig to generate the
single number of covariance matrix as shown in manual? I have used to input
only one eigenvec.trr and eigenval.xvg, then it is right to do this?

6. I have used eigenval.xvg as input file in g_anaeig which do not shows
nothing when used to open in xmgrace. Then how this file used for generating
eigcomp.xvg, proj.xvg, eigrmsf.xvg, 2dproj.xvg, 3dproj.pdb (which I have
successfully generated).

7. One last question is related to g_analyze that it reads ascii file and
analyze data sets, but in actual it used some graph.xvg file as input. I am
confused about this graph.xvg file which file should I used for input to
calculate the cosine content of the principal components.

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[gmx-users] RMSIP

[pawan raghav]

Thanks mark, but I think that g_anaeig calculates the degree of overlap then
what method would you use to calculate this?

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[gmx-users] RMSIP (Root mean square inner products)?

[pawan raghav]

Please tell me how gromacs calculates degree of overlap between
conformational spaces of the two proteins is it from RMSIP (Root mean square
inner products)? if yes then give me the reference in gromacs tutorial 4.0

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[gmx-users] PCA

[pawan raghav]

I have a little concept problem regarding principal component analysis. So
my question is about ED sampling are as follows:

1. I have read from the manual that g_covar calculates and diagonalize the
(mass-weighted) covariance matrix. So what is the meaning of mass-weighted
in covariance matrix?

2. g_covar output the eigenval.xvg and and eigenvec.trr, but when I opened
the eigenval.xvg file it will shows nothing, i don't know what was wrong
with it?

3. what is the difference between covariance matrix and normal mode analysis
because both were used to generate the eigenval.xvg and eigenvec.trr file?

4. g_anaeig analyze the eigenvectors, so it is possible to fitted all the
structures generated at the time of simulations of single structure without
using the other structure?

I mean to say that it is possible to use single structure as initial to
simulate and ED sampling?

5. what is the need of eigenvec2.trr input file in g_anaeig to generate the
single number of covariance matrix as shown in manual? I have used to input
only one eigenvec.trr and eigenval.xvg, then it is right to do this?

6. I have used eigenval.xvg as input file in g_anaeig which do not shows
nothing when used to open in xmgrace. Then how this file used for generating
eigcomp.xvg, proj.xvg, eigrmsf.xvg, 2dproj.xvg, 3dproj.pdb (which I have
were successfully generated).

7. One last question is related to g_analyze that it reads ascii file and
analyze data sets, but in actual it used some graph.xvg file as input. I am
confused about this graph.xvg file which file should I used for input to
calculate the cosine content of the principal components.

-- 
Pawan
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[gmx-users] Potein-protein complex simulations

[pawan raghav]

Dear users,
  I am using gromacs to understand the protein-protein
complex interaction stability prediction. for this I have used
protein-protein docked complex as initial .pdb file to simulate. According
to gromacs drug enzyme complex 3.3.1 tutorial, the .itp file needed as input
for drug molecule as seperate from protein file. So please tell me is
this compulsory to use small molecule as seperate, or can I perform MD
simulation by taking complex structure as directly. I am little confuse
about to do this because if I choose this then problem will occurs with
calculating the g_hbond. the g_hbond analyze the H-bonds between the complex
and with complex only. But I am intrested to calculate the H-bonds between
the protein (receptor) and and protein (ligand). Please notify me how can I
make this possible if no then tell me how to make .itp file of protein
(ligand) without using PRODRUG2 SERVER. Because prodrug server produced the
.itp file other than default amino acids example DRG.
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[gmx-users] g_sas

[pawan raghav]

*I executed the following command.
**
**g_sas -s mdrun.tpr -f mdrun.trr -or mdrun.xvg
***
**
*xmgrace -nxy mdrun.xvg*

*I get two sets of values: one is bigger (black) than the other (red).
***
*I have checked the manual and other sources, but I could not find an
**answer about the black and red line.  If it was written in fine print and
I missed it, I am sorry
**about that. So I want to know is the red lower value, the standard error
or standard deviation or
something else? What does red and black line shows also link the reference.*
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[gmx-users] MD simulations with multiple structures

[pawan raghav]

Dear Justin,

I want to know about
1. How to run MD simulations with multiple structures?

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[gmx-users] How to insput more than two PDB files to use for MD run

[pawan raghav]

Dear,

Is it possible to compare more than two pdb files MD simulations in a single
run? how?

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[gmx-users] GRACE

[pawan raghav]

Hi,

Please tell me how to install GRACE source files to execute xmgrace command
to visualize 2D graph. I am unable to installed it as read from tutorial.
please help me as I am in need.


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[gmx-users] gmx-GRACE problem

[pawan raghav]

Hi friends I want to know about which should be downloaded to use GRACE.

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[gmx-users] Hi

[pawan raghav]

Which files should be downloaded to use GRACE and in which directory should
be installed to use xmgrace command.

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[gmx-users] Problems

[pawan raghav]

When defining the box dimention then how do I know about the distance of
protein from the box wall? Which should be greater than half of the Cut-Off
(1.4nm) (according to some tutorial).

Then what are longest cutoff which must be shorter than half the shortest
box vector to satisfy the minimum image convention. I am asking because I
have run gromacs from default parameter of some other tutorial. I have used
0.75 value for -d when using editconf.

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[gmx-users] xmgrace

[pawan raghav]

While running MD simulation I have number of queries mentioned below:

1. When executing xmgrace command it returns the bash command not found,
then how to install GRACE package on windows?
2. When defining the box dimention then how do I know about the distance of
protein (207 residues) from the box wall should be greater than half of the
Cut-Off (1.4nm)?
3. In fullmd_sol.mdp file how to find the time step value because I don't
have confirmation about that.
4. When using grommp command to generate fullmd.tpr file, it will shows 3
notes
(a.) The Berendsen thermostat does not generate
the correct K.E distribution, and suggesting to use v- rescale thermostat
(b.) Why the system has non-zero total charge :
-2.01e+00
(c.) [file fullmd_sol.mdp, line unknow]: you are
using a plain coulomb cut-off, which might produce artifacts. You might want
to consider using PME   electostatics.
5. How to save screen of cygwin (general question)

Please solve these problems if you can I am thankful to you.

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[gmx-users] gromacs error

[pawan raghav]

I am using Gromacs on windows hen executing pdb2gmx command, I got an error
i.e.

Fatal error: Atom HD1 in residue HISB 3 not found in rtp entry with 14 atoms
while sorting atoms. May be different protonation state. Remove this
hydrogen or choose a different protonation state.

I want to know what is the error type and where is rtp entry.

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[gmx-users] (no subject)

[pawan raghav]

I have used GROMACS 4.0.5 on windows can anyone tell me about how to get
em.mdp, and pr.mdp file for my protein.

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[gmx-users] (no subject)

[pawan raghav]

After installing gromacs4.0 on windows it created Gromacs directory
containing several  .exe files in bin directory. But when I used pdb2gmx
command it will shows that basch command is not found. So anyone can tell me
what is that.

-- 
Pawan Kumar Raghav
Bioinformatician
Stem Cell and Gene Therapy Research Group
INMAS, DRDO
Timarpur Delhi-110054
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[gmx-users] gmx user

[pawan raghav]

Hello Users,

I am trying to install gromacs on windows and find lot of problems. First I
have installed Cygwin with gcc, gdb and make packages. Then FFTW-3.2.2 and
configure it but when I used make and make install commands but some
directories leave as it is. When configure gromacs-4.0.5 then it will shows
error in configuration  file line no 14 and 25 about $ '/r' command not
found and syntax error. so please tell me the solution.

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[gmx-users] gmx user

[pawan raghav]

Dear all,

I am a new user of GROMACS and suffering from severe problem about
fftw-3.2.2 installation. Actually I have installed cygwin on windows XP with
gcc, gdb, and make packages rest all are leaved default. Now when I have
used configure command then it would give last line as

config.status: executing libtool commands

then returned back to my current working directory, after that when used
make command it gives an error i.e.

../libtool: line 111: CDPATH: command not found
libtool: Version mismatch error. This is libtool 2.2.6 Debian-2.2.6a-4 but
the
 libtool: definition of this LT_INIT comes from an older release.
 libtool: You should recreate aclocal.m4 with macros from libtool 2.2.6
 libtool: and run autoconf again.
 make[2]: *** [align.lo] Error 63
 make[2]: Leaving directory `/cygdrive/c/fftw-3.2.2/kernel
 make[1]: *** [all-recursive] Error 1
 make[1]: Leaving directory `/cygdrive/c/fftw-3.2.2/'
 make: *** [all] Error 2


So friends I will be very thankful if anybody help me.


with regards
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Pawan Kumar Raghav
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