Re: [gmx-users] how to indicate solvent flexibility?

[Albert]

Hello Justin and Leandro:

  thanks a lot for kind advices. I am trying to us the g_msd to 
calculate the density:


first I made a index file called density.ndx with g_select, defined the 
solvent within 6A of a residue


after that I try to run g_msd with command:

g_msd_mpi -f md.xtc -s analysis.tpr -n density.ndx -mol diff_mol.xvg -o 
msd.xvg


a dialoug popped up with above command:


.
Group 13963 (close_27926.000) has 7 elements
Group 13964 (close_27928.000) has 5 elements
Group 13965 (close_27930.000) has 7 elements
Group 13966 (close_27932.000) has 7 elements
Group 13967 (close_27934.000) has 7 elements
Group 13968 (close_27936.000) has 8 elements
Group 13969 (close_27938.000) has 9 elements
Group 13970 (close_27940.000) has 6 elements
Group 13971 (close_27942.000) has 9 elements
Group 13972 (close_27944.000) has 9 elements
Group 13973 (close_27946.000) has 9 elements
Group 13974 (close_27948.000) has10 elements
Group 13975 (close_27950.000) has 9 elements
Group 13976 (close_27952.000) has12 elements
Group 13977 (close_27954.000) has10 elements
Group 13978 (close_27956.000) has 9 elements
Group 13979 (close_27958.000) has10 elements
Group 13980 (close_27960.000) has 8 elements
Group 13981 (close_27962.000) has10 elements
Group 13982 (close_27964.000) has10 elements
Group 13983 (close_27966.000) has 7 elements
Group 13984 (close_27968.000) has 9 elements
Group 13985 (close_27970.000) has 8 elements
Group 13986 (close_27972.000) has 8 elements
Group 13987 (close_27974.000) has 7 elements
Group 13988 (close_27976.000) has 9 elements
Group 13989 (close_27978.000) has 6 elements
Group 13990 (close_27980.000) has 9 elements
Group 13991 (close_27982.000) has 8 elements
Group 13992 (close_27984.000) has 8 elements
Group 13993 (close_27986.000) has11 elements
Group 13994 (close_27988.000) has10 elements
Group 13995 (close_27990.000) has11 elements
Group 13996 (close_27992.000) has10 elements
Group 13997 (close_27994.000) has11 elements
Group 13998 (close_27996.000) has11 elements
Group 13999 (close_27998.000) has 9 elements
Group 14000 (close_28000.000) has12 elements


I select 14000 which is the last one, but it failed with messages:

rogram g_msd_mpi, VERSION 4.5.5-dev-20121121-3e633d4
Source code file: /home/albert/software/gromacs/src/tools/gmx_msd.c, 
line: 739


Fatal error:
The index group does not consist of whole molecules
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Can't You Make This Thing Go Faster ? (Black Crowes)


thank you very much
Albert





On 01/08/2013 06:15 PM, Justin Lemkul wrote:



On 1/8/13 11:42 AM, Albert wrote:

hello:

   I've finished a 60ns MD simulation with Gromacs and I found that the
flixbility of solvent molecules inside the protein is different when 
it binds
with different ligands: ie. in one case the solvent can move very 
fast with bulk
environment, and in other case the solvent forms type Hbonds with 
resdiues
inside protein.  I am just wondering how which module of Gromacs can 
I use to
indicate the solvent difference in flexibility? Is it possible to 
calculate the

entropy in certain region (let's say: 20Z30 ) of the solvent?



It sounds like g_rmsf and g_msd may be useful here.  The only way to 
specify geometric criteria for index groups is to use g_select, but 
then the analysis has to be done on each individual frame, not the 
trajectory.  Dynamic selections will be more conveniently implemented 
in a future Gromacs version.


-Justin



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Re: [gmx-users] how to indicate solvent flexibility?

[David van der Spoel]

On 2013-01-10 10:45, Albert wrote:

Hello Justin and Leandro:

   thanks a lot for kind advices. I am trying to us the g_msd to
calculate the density:


try g_msd -h
wrong tool.



first I made a index file called density.ndx with g_select, defined the
solvent within 6A of a residue

after that I try to run g_msd with command:

g_msd_mpi -f md.xtc -s analysis.tpr -n density.ndx -mol diff_mol.xvg -o
msd.xvg

a dialoug popped up with above command:


.
Group 13963 (close_27926.000) has 7 elements
Group 13964 (close_27928.000) has 5 elements
Group 13965 (close_27930.000) has 7 elements
Group 13966 (close_27932.000) has 7 elements
Group 13967 (close_27934.000) has 7 elements
Group 13968 (close_27936.000) has 8 elements
Group 13969 (close_27938.000) has 9 elements
Group 13970 (close_27940.000) has 6 elements
Group 13971 (close_27942.000) has 9 elements
Group 13972 (close_27944.000) has 9 elements
Group 13973 (close_27946.000) has 9 elements
Group 13974 (close_27948.000) has10 elements
Group 13975 (close_27950.000) has 9 elements
Group 13976 (close_27952.000) has12 elements
Group 13977 (close_27954.000) has10 elements
Group 13978 (close_27956.000) has 9 elements
Group 13979 (close_27958.000) has10 elements
Group 13980 (close_27960.000) has 8 elements
Group 13981 (close_27962.000) has10 elements
Group 13982 (close_27964.000) has10 elements
Group 13983 (close_27966.000) has 7 elements
Group 13984 (close_27968.000) has 9 elements
Group 13985 (close_27970.000) has 8 elements
Group 13986 (close_27972.000) has 8 elements
Group 13987 (close_27974.000) has 7 elements
Group 13988 (close_27976.000) has 9 elements
Group 13989 (close_27978.000) has 6 elements
Group 13990 (close_27980.000) has 9 elements
Group 13991 (close_27982.000) has 8 elements
Group 13992 (close_27984.000) has 8 elements
Group 13993 (close_27986.000) has11 elements
Group 13994 (close_27988.000) has10 elements
Group 13995 (close_27990.000) has11 elements
Group 13996 (close_27992.000) has10 elements
Group 13997 (close_27994.000) has11 elements
Group 13998 (close_27996.000) has11 elements
Group 13999 (close_27998.000) has 9 elements
Group 14000 (close_28000.000) has12 elements


I select 14000 which is the last one, but it failed with messages:

rogram g_msd_mpi, VERSION 4.5.5-dev-20121121-3e633d4
Source code file: /home/albert/software/gromacs/src/tools/gmx_msd.c,
line: 739

Fatal error:
The index group does not consist of whole molecules
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Can't You Make This Thing Go Faster ? (Black Crowes)


thank you very much
Albert





On 01/08/2013 06:15 PM, Justin Lemkul wrote:



On 1/8/13 11:42 AM, Albert wrote:

hello:

   I've finished a 60ns MD simulation with Gromacs and I found that the
flixbility of solvent molecules inside the protein is different when
it binds
with different ligands: ie. in one case the solvent can move very
fast with bulk
environment, and in other case the solvent forms type Hbonds with
resdiues
inside protein.  I am just wondering how which module of Gromacs can
I use to
indicate the solvent difference in flexibility? Is it possible to
calculate the
entropy in certain region (let's say: 20Z30 ) of the solvent?



It sounds like g_rmsf and g_msd may be useful here.  The only way to
specify geometric criteria for index groups is to use g_select, but
then the analysis has to be done on each individual frame, not the
trajectory.  Dynamic selections will be more conveniently implemented
in a future Gromacs version.

-Justin






--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell  Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] how to indicate solvent flexibility?

[Albert]

On 01/10/2013 11:14 AM, David van der Spoel wrote:

On 2013-01-10 10:45, Albert wrote:

Hello Justin and Leandro:

   thanks a lot for kind advices. I am trying to us the g_msd to
calculate the density:


try g_msd -h
wrong tool.


that's strange. Here is the information which I think it is what I want.


g_msd -h


DESCRIPTION
---
g_msd computes the mean square displacement (MSD) of atoms from a set of
initial positions. This provides an easy way to compute the diffusion
constant using the Einstein relation. The time between the reference points
for the MSD calculation is set with -trestart. The diffusion constant is
calculated by least squares fitting a straight line (D*t + c) through the
MSD(t) from -beginfit to -endfit (note that t is time from the reference
positions, not simulation time). An error estimate given, which is the
difference of the diffusion coefficients obtained from fits over the two
halves of the fit interval.

There are three, mutually exclusive, options to determine different types of
mean square displacement: -type, -lateral and -ten. Option -ten writes the
full MSD tensor for each group, the order in the output is: trace xx yy 
zz yx

zx zy.

If -mol is set, g_msd plots the MSD for individual molecules (including
making molecules whole across periodic boundaries): for each individual
molecule a diffusion constant is computed for its center of mass. The chosen
index group will be split into molecules.

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Re: [gmx-users] how to indicate solvent flexibility?

[Justin Lemkul]

On 1/10/13 5:21 AM, Albert wrote:

On 01/10/2013 11:14 AM, David van der Spoel wrote:

On 2013-01-10 10:45, Albert wrote:

Hello Justin and Leandro:

   thanks a lot for kind advices. I am trying to us the g_msd to
calculate the density:


try g_msd -h
wrong tool.


that's strange. Here is the information which I think it is what I want.



David's point was that g_msd does not calculate density, which you stated was 
what you were trying to do.


-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] how to indicate solvent flexibility?

[Justin Lemkul]

On 1/10/13 4:45 AM, Albert wrote:

Hello Justin and Leandro:

   thanks a lot for kind advices. I am trying to us the g_msd to calculate the
density:

first I made a index file called density.ndx with g_select, defined the solvent
within 6A of a residue

after that I try to run g_msd with command:

g_msd_mpi -f md.xtc -s analysis.tpr -n density.ndx -mol diff_mol.xvg -o msd.xvg

a dialoug popped up with above command:


.
Group 13963 (close_27926.000) has 7 elements
Group 13964 (close_27928.000) has 5 elements
Group 13965 (close_27930.000) has 7 elements
Group 13966 (close_27932.000) has 7 elements
Group 13967 (close_27934.000) has 7 elements
Group 13968 (close_27936.000) has 8 elements
Group 13969 (close_27938.000) has 9 elements
Group 13970 (close_27940.000) has 6 elements
Group 13971 (close_27942.000) has 9 elements
Group 13972 (close_27944.000) has 9 elements
Group 13973 (close_27946.000) has 9 elements
Group 13974 (close_27948.000) has10 elements
Group 13975 (close_27950.000) has 9 elements
Group 13976 (close_27952.000) has12 elements
Group 13977 (close_27954.000) has10 elements
Group 13978 (close_27956.000) has 9 elements
Group 13979 (close_27958.000) has10 elements
Group 13980 (close_27960.000) has 8 elements
Group 13981 (close_27962.000) has10 elements
Group 13982 (close_27964.000) has10 elements
Group 13983 (close_27966.000) has 7 elements
Group 13984 (close_27968.000) has 9 elements
Group 13985 (close_27970.000) has 8 elements
Group 13986 (close_27972.000) has 8 elements
Group 13987 (close_27974.000) has 7 elements
Group 13988 (close_27976.000) has 9 elements
Group 13989 (close_27978.000) has 6 elements
Group 13990 (close_27980.000) has 9 elements
Group 13991 (close_27982.000) has 8 elements
Group 13992 (close_27984.000) has 8 elements
Group 13993 (close_27986.000) has11 elements
Group 13994 (close_27988.000) has10 elements
Group 13995 (close_27990.000) has11 elements
Group 13996 (close_27992.000) has10 elements
Group 13997 (close_27994.000) has11 elements
Group 13998 (close_27996.000) has11 elements
Group 13999 (close_27998.000) has 9 elements
Group 14000 (close_28000.000) has12 elements



Each of these groups corresponds to the atoms that satisfied the g_select 
criteria for a given frame.  That may not continuously apply to what you 
actually want to measure.




I select 14000 which is the last one, but it failed with messages:

rogram g_msd_mpi, VERSION 4.5.5-dev-20121121-3e633d4
Source code file: /home/albert/software/gromacs/src/tools/gmx_msd.c, line: 739

Fatal error:
The index group does not consist of whole molecules
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---



So make an index file that contains intact molecules.  That's a prerequisite for 
using the -mol flag.


-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] how to indicate solvent flexibility?

[Albert]

hello:

  I've finished a 60ns MD simulation with Gromacs and I found that the 
flixbility of solvent molecules inside the protein is different when it 
binds with different ligands: ie. in one case the solvent can move very 
fast with bulk environment, and in other case the solvent forms type 
Hbonds with resdiues inside protein.  I am just wondering how which 
module of Gromacs can I use to indicate the solvent difference in 
flexibility? Is it possible to calculate the entropy in certain region 
(let's say: 20Z30 ) of the solvent?


thank you very much
best
Albert
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Re: [gmx-users] how to indicate solvent flexibility?

[Justin Lemkul]

On 1/8/13 11:42 AM, Albert wrote:

hello:

   I've finished a 60ns MD simulation with Gromacs and I found that the
flixbility of solvent molecules inside the protein is different when it binds
with different ligands: ie. in one case the solvent can move very fast with bulk
environment, and in other case the solvent forms type Hbonds with resdiues
inside protein.  I am just wondering how which module of Gromacs can I use to
indicate the solvent difference in flexibility? Is it possible to calculate the
entropy in certain region (let's say: 20Z30 ) of the solvent?



It sounds like g_rmsf and g_msd may be useful here.  The only way to specify 
geometric criteria for index groups is to use g_select, but then the analysis 
has to be done on each individual frame, not the trajectory.  Dynamic selections 
will be more conveniently implemented in a future Gromacs version.


-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] how to indicate solvent flexibility?

[Leandro Bortot]

 My first thought was to compare the diffusion of the bulk and internal
waters with g_msd.

 You said that in some case the internal waters forms hydrogen bonds
with the protein. I think that in this case a plot showing this would be
nice too.


2013/1/8 Justin Lemkul jalem...@vt.edu



 On 1/8/13 11:42 AM, Albert wrote:

 hello:

I've finished a 60ns MD simulation with Gromacs and I found that the
 flixbility of solvent molecules inside the protein is different when it
 binds
 with different ligands: ie. in one case the solvent can move very fast
 with bulk
 environment, and in other case the solvent forms type Hbonds with resdiues
 inside protein.  I am just wondering how which module of Gromacs can I
 use to
 indicate the solvent difference in flexibility? Is it possible to
 calculate the
 entropy in certain region (let's say: 20Z30 ) of the solvent?


 It sounds like g_rmsf and g_msd may be useful here.  The only way to
 specify geometric criteria for index groups is to use g_select, but then
 the analysis has to be done on each individual frame, not the trajectory.
  Dynamic selections will be more conveniently implemented in a future
 Gromacs version.

 -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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