You can also try:
gmxdump -f em.trr | & grep precision
Inon Sharony wrote:
> The *.gro file always has 3 significant digits, but the *.tpr file
> sometimes has the coordinates with 5 significant digits and sometimes
> the last two of those are zero.
>
>
> Quoting "Ran Friedman" <[EMAIL PROTECTED]>
The *.gro file always has 3 significant digits, but the *.tpr file
sometimes has the coordinates with 5 significant digits and sometimes
the last two of those are zero.
Quoting "Ran Friedman" <[EMAIL PROTECTED]>:
How do I get a *.gro file in double-precision, then? The
configurations giv
> How do I get a *.gro file in double-precision, then? The
> configurations given by the PRODRG server are in 0.000 format, and
> still I've at least once managed to get double-precision calculations
> out of them (right now I'm working on a file for a Pentane molecule,
> originally downloaded fro
Quoting "Ran Friedman" <[EMAIL PROTECTED]>:
Inon Sharony wrote:
Dear Ran,
I'm still unsure of why I sometimes can get double-precision
output
and sometimes not. I can't find what I'm doing differently in each
case, however I now know what to look for in order to be sure that
I'm
getting wh
Inon Sharony wrote:
> Dear Ran,
>
> I'm still unsure of why I sometimes can get double-precision output
> and sometimes not. I can't find what I'm doing differently in each
> case, however I now know what to look for in order to be sure that I'm
> getting what I need. Obviously, the need for double
Dear Ran,
I'm still unsure of why I sometimes can get double-precision output
and sometimes not. I can't find what I'm doing differently in each
case, however I now know what to look for in order to be sure that I'm
getting what I need. Obviously, the need for double-precision stems
only
Inon Sharony wrote:
> This is exactly the point - I get only three significant digits.
> Although I performed the entire procedure in double-precision. The
> convergence to 5E-4 DID occur in single-precision, I just thought it
> wasn't good enough (the program recommends 1E-5 and when
> double-prec
This is exactly the point - I get only three significant digits.
Although I performed the entire procedure in double-precision. The
convergence to 5E-4 DID occur in single-precision, I just thought it
wasn't good enough (the program recommends 1E-5 and when
double-precision works for me I g
Hi Inon,
Check the files after EM. How many significant digits do you have? I
guess you wouldn't get a convergence to 5E-4 with single precision. From
my experience it may be worth to run several cycles of EM, say CG and
then L-BFGS to get better convergence.
Ran.
Inon Sharony wrote:
> I now pe
I now performed:
make distclean
./configure --disable-float
make
make install
make links
All executed without problems. Now I no longer have segmentation
faults (thanks David!), however the energy minimization still does not
achieve 1E-05 kJ / mole nm convergence (only as good as ~5E-04 for
>
>Could it be that this, second, compilation might have caused some
>problems -- I had GROMACS compiled in single-precision, and it worked
>fine -- could compiling in double-precision after the initial
>single-precision overrun some files? I'm not sure anymore...
>
from experien
I think we're getting somewhere...
when I look at the *.tpr file, under the line
nosehoover_xi: 0
I have the x[ 0] etc. lines, but they are as you described single
precision should look like (the last two digits are all zeros). This
is despite the fact that at the top it sa
Ran Friedman wrote:
> Inon Sharony wrote:
>
>> Hi Ran.
>> I looked up your suggestions, and got the following:
>>
>> 0. The parameters in the *.tpr file appear in " 0.e+00 "
>> format. How can I tell if this is a float or double? Also, I could not
>> see if the position coordinates of th
Inon Sharony wrote:
> Hi Ran.
> I looked up your suggestions, and got the following:
>
> 0. The parameters in the *.tpr file appear in " 0.e+00 "
> format. How can I tell if this is a float or double? Also, I could not
> see if the position coordinates of the molecule appear in the *.tpr
>
Hi Ran.
I looked up your suggestions, and got the following:
0. The parameters in the *.tpr file appear in " 0.e+00 "
format. How can I tell if this is a float or double? Also, I could not
see if the position coordinates of the molecule appear in the *.tpr
file (and if so, if they a
Inon Sharony wrote:
>
> Hi Ran, thanks for the reply
>
> I ran "make tests" after compiling with double precision, and it came
> out fine.
>
> Could it be that this, second, compilation might have caused some
> problems -- I had GROMACS compiled in single-precision, and it worked
> fine -- could c
Hi Ran, thanks for the reply
I ran "make tests" after compiling with double precision, and it came out fine.
Could it be that this, second, compilation might have caused some problems -- I
had GROMACS compiled in single-precision, and it worked fine -- could compiling
in double-precision a
Hi,
It's hard to know why you get a segmentation fault without further info.
Did you ran the GMX tests after installation with double precision? Is
everything all right there?
Also, when exactly the system crashes? Is it straight when you start
mdrun? Did you use both grompp and mdrun in double p
Hi all!
I'm trying to perform a normal mode (NM) analysis, but having trouble with the
recommendation of first performing a double precision energy
minimization before writing
the Hessian. The calculation of the Hessian matrix is done using
mdrun, and its
diagonalization is done using g_nmeig
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