You can put whichever spin you like into what is said, but there is a clear
(and unnecessary) fault with the way coordinates are stored in gro files
when made from pdb using pdb2gmx.
On Sun, Nov 27, 2011 at 12:39 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 27/11/2011 5:07 AM, Igor Druz
My my. Why is it a fault to adhere to ISO units (nm) over non-standard
(A)? It's a choice, but a choice is not faulty. The consequences may
be undesirable. But shouldn't a user, certainly a computation
scientist, understand the file formats, as an experimentalist should
know its solvent? And know
You are missing the point. Quoting my response to David:
I appreciate the history of the matter, but it would save a lot of headache
to store coordinates in angstroms in gro files, i.e., not to omit 2 in
4.172 A in the pdb file by converting it to 0.417 nm in the gro file. What
is the point in
Hi Igor,
Please do read the manual. The GRO file format is a fixed-width format
with %8.3f for coordinates, velocities and forces. Changing the format
to %9.4f will break everything written in fortran. And, yes, people
still use fortran. So which point did I miss? :)
Cheers,
Tsjerk
On Sun,
write to gro in angstroms, read from gro in angstroms, convert into nm in
grompp.
On Sun, Nov 27, 2011 at 10:41 AM, Tsjerk Wassenaar tsje...@gmail.comwrote:
Hi Igor,
Please do read the manual. The GRO file format is a fixed-width format
with %8.3f for coordinates, velocities and forces.
On 2011-11-27 12:15, Igor Druz wrote:
write to gro in angstroms, read from gro in angstroms, convert into nm
in grompp.
once more you don't have to use gro, use g96 if precision is important.
if we'd introduce a gro format in angstrom it couldn't be called .gro
anyway since that would confuse
On 27/11/2011 10:15 PM, Igor Druz wrote:
write to gro in angstroms, read from gro in angstroms, convert into nm
in grompp.
What are you trying to communicate with this hypothetical workflow?
Historical file formats imply particular units and are often limited to
a particular precision.
On Sun, Nov 27, 2011 at 11:26 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 27/11/2011 10:15 PM, Igor Druz wrote:
write to gro in angstroms, read from gro in angstroms, convert into nm in
grompp.
What are you trying to communicate with this hypothetical workflow?
Historical file
Back to square one! The point you are missing is that 4.172 A is not
equal to 0.417 nm and pdb2gmx does it without any warning.
You have a point. It is not possible to change the file formats without
creating great havoc as I'm sure you understand, but a warning that
precision is lost
There is something not quite right here.
I grompp a gro file created from a pdb file using pdb2gmx and run MD to do
a single point energy calculation.
I then grompp the original pdb file and run MD to do a single point energy
calculation.
The values of potential energy values are different by
It's more useful if you provide more information. What was the .pdb
file (can I download it from the pdb databank?) was there water? what
version of gromacs? was it compiled in double or single precision?
what were your mdp parameters?
-- original message --
There is something not quite
There was no water. Version 4.5.5. Single precision. This is what I ran:
pdb2gmx -f 1.pdb -p g1 -o g1
grompp -f 1.mdp -c g1.gro -o g1.tpr -p g1.top
mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene
Potential energy: 1.19780e+02 kJ/mol
grompp -f 1.mdp -c 1.pdb -o g1.tpr -p g1.top
mdrun -v -s
On 2011-11-26 16:38, Igor Druz wrote:
There was no water. Version 4.5.5. Single precision. This is what I ran:
pdb2gmx -f 1.pdb -p g1 -o g1
grompp -f 1.mdp -c g1.gro -o g1.tpr -p g1.top
mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene
Potential energy: 1.19780e+02 kJ/mol
grompp -f 1.mdp -c
There is rounding because of angstroms vs nanometers and both files
maintain 3 decimal places (see below).
The intention of pdb2gmx is not to get a .gro , but to get a .top or
.itp file.
I see your point, but I don't think it matters. If you really need
that precision, then I'd think
I already knew the reason. But I had to find this out hard way. Now facing
a dreading prospect of repeating tons of calculations! Hence the request
for the bad for the health sign. Btw, gromacs issues a lot of warnings,
but not this one :D
What a bright idea to switch from angstroms to
1. why repeat the calculations? If you're talking about simulations
then there is no need to repeat them due to this. You will get
different answers with the same starting coordinates if you simply
change the initial velocities. If you're talking about instantaneous
energy calculations
On Sat, Nov 26, 2011 at 5:35 PM, chris.ne...@utoronto.ca wrote
1. why repeat the calculations? If you're talking about simulations then
there is no need to repeat them due to this. You will get different answers
with the same starting coordinates if you simply change the initial
velocities.
On 2011-11-26 19:07, Igor Druz wrote:
On Sat, Nov 26, 2011 at 5:35 PM, chris.ne...@utoronto.ca
mailto:chris.ne...@utoronto.ca wrote
1. why repeat the calculations? If you're talking about simulations
then there is no need to repeat them due to this. You will get
different answers
On Sat, Nov 26, 2011 at 6:37 PM, David van der Spoel
sp...@xray.bmc.uu.sewrote:
On 2011-11-26 19:07, Igor Druz wrote:
On Sat, Nov 26, 2011 at 5:35 PM, chris.ne...@utoronto.ca
mailto:chris.neale@utoronto.**ca chris.ne...@utoronto.ca wrote
1. why repeat the calculations? If you're talking
On 2011-11-26 20:15, Igor Druz wrote:
On Sat, Nov 26, 2011 at 6:37 PM, David van der Spoel
sp...@xray.bmc.uu.se mailto:sp...@xray.bmc.uu.se wrote:
On 2011-11-26 19:07, Igor Druz wrote:
On Sat, Nov 26, 2011 at 5:35 PM, chris.ne...@utoronto.ca
mailto:chris.ne...@utoronto.ca
On 27/11/2011 5:07 AM, Igor Druz wrote:
On Sat, Nov 26, 2011 at 5:35 PM, chris.ne...@utoronto.ca
mailto:chris.ne...@utoronto.ca wrote
1. why repeat the calculations? If you're talking about
simulations then there is no need to repeat them due to this. You
will get different answers
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