Re: [gmx-users] Normal Mode Analysis starting from an optimized geometry and known partial charges
On 12/21/2011 12:57 AM, Thomas Evangelidis wrote:
Mark, thanks for the prompt response!
I have done Normal Mode Analysis and have calculated partial
charges and the optimized geometry of a few compounds using
high-level QM calculations. Now I want to see (if possible) how
well GROMACS can reproduce the normal modes if I start from the
same optimized geometry and use the same partial charges.
In general for NMA to make sense you need to be at a stationary
point w.r.t. the atomic degrees of freedom of the model being
used. That won't be quite true at a QM geometry, so there's a
sense of apples-vs-oranges comparison.
If I get it right you mean that NMA in GROMACS must start from an
energy minimum (stationary point) w.r.t the ff used (GAFF in my case),
which means that an energy minimization is neccessary ever if I use an
QM optimum geometry and the respective partial charges. Namely there
is no way to reproduce the normal modes I obtained from QM
calculations, correct?
You can choose to compare the two models on the same configuration, or
at the local minimum w.r.t. each model that is nearest some
configuration. Each approach has a minor flaw. How you need to manage
precision varies with the choice you make.
An obvious problem is that the starting compound geometry is not
in full precision
The starting geometry is in full precision if it's the same as
that used for the QM calculation. That is quite possible to
achieve with .pdb or .gro input.
The same as the starting geometry or as the optimized geometry?
Your choice - your original workflow did no EM in GROMACS, so the use of
.trr format was immaterial.
as highlighted in the documentation:
http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis
Is it possible to create a full precision .trr coordinate file
from a .gro or any other structure file with modified 8-decimal
point coordinates?
I think you are misunderstanding the use of the word "precision"
here. In general, the same configuration will be represented
differently in .trr and .gro formats, with the former being a
closer approximation. Accordingly, one will get a different result
for NMA on the endpoint of GROMACS EM as observed in the .trr file
and as observed in the .gro file. The former will be closer to the
stationary point, and so lead to more acceptable estimates of the
normal modes. However, here you want to do NMA on the same
coordinates with two programs, so it is up to you to represent the
coordinates in a way that the two programs can compute on the same
approximation to the coordinates of the stationary point. There's
no need to convert to .trr (or the QM binary format), because all
that does is treat 2.613 as 2.613.
So a command line like this will do the job, right?
grompp_d4.5.5 -f nm.mdp -c ${ligand}_8_decimal_points.gro -p
${ligand}.top -o nm.tpr
That copies the configuration in -c in the full precision available from
the format of -c into the .tpr.
Mark
--
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Normal Mode Analysis starting from an optimized geometry and known partial charges
Mark, thanks for the prompt response!
I have done Normal Mode Analysis and have calculated partial charges and
> the optimized geometry of a few compounds using high-level QM calculations.
> Now I want to see (if possible) how well GROMACS can reproduce the normal
> modes if I start from the same optimized geometry and use the same partial
> charges.
>
>
> In general for NMA to make sense you need to be at a stationary point
> w.r.t. the atomic degrees of freedom of the model being used. That won't be
> quite true at a QM geometry, so there's a sense of apples-vs-oranges
> comparison.
>
>
If I get it right you mean that NMA in GROMACS must start from an energy
minimum (stationary point) w.r.t the ff used (GAFF in my case), which means
that an energy minimization is neccessary ever if I use an QM optimum
geometry and the respective partial charges. Namely there is no way to
reproduce the normal modes I obtained from QM calculations, correct?
> An obvious problem is that the starting compound geometry is not in full
> precision
>
> The starting geometry is in full precision if it's the same as that used
> for the QM calculation. That is quite possible to achieve with .pdb or .gro
> input.
>
>
The same as the starting geometry or as the optimized geometry?
> as highlighted in the documentation:
>
> http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis
>
> Is it possible to create a full precision .trr coordinate file from a .gro
> or any other structure file with modified 8-decimal point coordinates?
>
>
> I think you are misunderstanding the use of the word "precision" here. In
> general, the same configuration will be represented differently in .trr and
> .gro formats, with the former being a closer approximation. Accordingly,
> one will get a different result for NMA on the endpoint of GROMACS EM as
> observed in the .trr file and as observed in the .gro file. The former will
> be closer to the stationary point, and so lead to more acceptable estimates
> of the normal modes. However, here you want to do NMA on the same
> coordinates with two programs, so it is up to you to represent the
> coordinates in a way that the two programs can compute on the same
> approximation to the coordinates of the stationary point. There's no need
> to convert to .trr (or the QM binary format), because all that does is
> treat 2.613 as 2.613.
>
>
So a command line like this will do the job, right?
grompp_d4.5.5 -f nm.mdp -c ${ligand}_8_decimal_points.gro -p ${ligand}.top
-o nm.tpr
Thomas
==
Thomas Evangelidis
PhD student
Biomedical Research Foundation, Academy of Athens
4 Soranou Ephessiou , 115 27 Athens, Greece
email: tev...@bioacademy.gr
teva...@gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Normal Mode Analysis starting from an optimized geometry and known partial charges
On 20/12/11, Thomas Evangelidis wrote:
> Dear GROMACS users,
>
>
> I have done Normal Mode Analysis and have calculated partial charges and the
> optimized geometry of a few compounds using high-level QM calculations. Now I
> want to see (if possible) how well GROMACS can reproduce the normal modes if
> I start from the same optimized geometry and use the same partial charges.
>
In general for NMA to make sense you need to be at a stationary point w.r.t.
the atomic degrees of freedom of the model being used. That won't be quite true
at a QM geometry, so there's a sense of apples-vs-oranges comparison.
> The command lines I use are the following:
>
>
> ligand="10058_F4.nw.new_GMX"
>
> ## do Normal Mode Analysis
> grompp_d4.5.5 -f nm.mdp -c ${ligand}.gro -p ${ligand}.top -o nm.tpr
> mdrun_d4.5.5 -v -deffnm nm
>
> ## calculate the eigenvectors/values of the Hessian matrix and write the
> eigenvectors to a trajectory file
>
> g_nmeig_d4.5.5 -f nm.mtx -s nm.tpr -of -ol -v -m -last 81
>
> ## plot the vector components and the RMS fluctuation per atom of
> eigenvectors for all eigenvectors
> echo 0 | g_anaeig_d4.5.5 -v eigenvec.trr -s nm.tpr -eig eigenval.xvg -comp
> -rmsf -last -1
>
>
> ## create a trajectory from the eigenvector 76 (the first 6 are the rotation
> and translation) to visualize the vibrations in VMD
> g_nmtraj_d4.5.5 -s nm.tpr -v eigenvec.trr -eignr "76" -nframes 10 -amplitude
> 1 -o
>
>
> Most of the resulting normal modes do not coincide with the respective ones
> calculated through QM. Does the order of the above command lines make sense?
>
>
> An obvious problem is that the starting compound geometry is not in full
> precision
>
The starting geometry is in full precision if it's the same as that used for
the QM calculation. That is quite possible to achieve with .pdb or .gro input.
> as highlighted in the documentation:
>
>
> http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis
>
> Is it possible to create a full precision .trr coordinate file from a .gro or
> any other structure file with modified 8-decimal point coordinates?
>
I think you are misunderstanding the use of the word "precision" here. In
general, the same configuration will be represented differently in .trr and
.gro formats, with the former being a closer approximation. Accordingly, one
will get a different result for NMA on the endpoint of GROMACS EM as observed
in the .trr file and as observed in the .gro file. The former will be closer to
the stationary point, and so lead to more acceptable estimates of the normal
modes. However, here you want to do NMA on the same coordinates with two
programs, so it is up to you to represent the coordinates in a way that the two
programs can compute on the same approximation to the coordinates of the
stationary point. There's no need to convert to .trr (or the QM binary format),
because all that does is treat 2.613 as 2.613.
Mark
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
