Re: [gmx-users] Essential Dynamics Sampling (EDS) MD
I've rerun everything from scratch following Bert's input. The numbers seemed all right, but the runs still failed. Then I tried using just a subset of the eigenvectors, which has worked so far (i.e. it's running for about 1ns). Bert and Lars - thanks a lot for your help, Ran. Bert de Groot wrote: > > then there's possibly some mixup between fitting reference and/or > selection > and/or the eigenvectors between g_anaeig and make_edi? > > Please make sure that group selections and reference groups (-s option > of make_edi, g_covar and g_anaeig) are identical. Check covar.log if > you're > not sure anymore which fitting structure/selection you chose for g_covar. > > If you still have problems, please feel free to contact me off-list > with a minimal > set of files with which the problem can be reproduced. > > cheers, > > Bert > ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Essential Dynamics Sampling (EDS) MD
Ran Friedman wrote: Dear Bert, The Jacobi error hints at a fitting problem. If not the starting position, could it be the target that's causing the problems? Please check the head of the .edo and log files, to see if the reported RMSD's are what you would expect and especially if reported projections are compatible with g_anaeig. Do you refer to EDx? The values are not equal to what I get from g_anaeig. then there's possibly some mixup between fitting reference and/or selection and/or the eigenvectors between g_anaeig and make_edi? Please make sure that group selections and reference groups (-s option of make_edi, g_covar and g_anaeig) are identical. Check covar.log if you're not sure anymore which fitting structure/selection you chose for g_covar. If you still have problems, please feel free to contact me off-list with a minimal set of files with which the problem can be reproduced. cheers, Bert __ Bert de Groot, PhD Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 37077 Goettingen, Germany tel: +49-551-2012308, fax: +49-551-2012302 http://www.mpibpc.mpg.de/groups/de_groot ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Essential Dynamics Sampling (EDS) MD
Dear Bert, > > The Jacobi error hints at a fitting problem. If not the starting > position, could it > be the target that's causing the problems? > > Please check the head of the .edo and log files, to see if the > reported RMSD's > are what you would expect and especially if reported projections are > compatible with > g_anaeig. Do you refer to EDx? The values are not equal to what I get from g_anaeig. Thanks, Ran. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Essential Dynamics Sampling (EDS) MD
Ran Friedman wrote:
Dear Lars, GMX users:
It doesn't seem to be the problem, as the initial RMSD from reference
structure =0.16037 nm
I also get:
The Jacobi error hints at a fitting problem. If not the starting position,
could it
be the target that's causing the problems?
Please check the head of the .edo and log files, to see if the reported RMSD's
are what you would expect and especially if reported projections are compatible
with
g_anaeig.
Large VCM(group rest): nan, nan, nan,
ekin-cm: nan
In the log file.
Ran.
Lars Schaefer wrote:
Dear Ran,
this could mean that you have problems fitting to your reference
structure.
Lars
Ran Friedman wrote:
Dear all,
I'm resending this message (please see below) with some additional
info, hoping that someone can at least point me to what I should check.
I ran the simulation with the -debug flag and got some "nan" values in
mdrun.log:
dekin = nan, ekin = 175815 vcm = ( nan nan nan)
mv = ( nan nan nan)
PC: pres (3x3):
PC: pres[0]={ nan, nan, nan}
PC: pres[1]={ nan, nan, nan}
PC: pres[2]={ nan, nan, nan}
PC: ekin (3x3):
PC: ekin[0]={ nan, nan, nan}
PC: ekin[1]={ nan, nan, nan}
PC: ekin[2]={ nan, nan, nan}
PC: vir (3x3):
PC: vir [0]={ 5.66646e+04, 1.12632e+02, -1.88577e+03}
PC: vir [1]={ 5.10852e+02, 5.71922e+04, 3.69013e+03}
PC: vir [2]={-1.82055e+03, 3.43891e+03, 6.20980e+04}
PC: box (3x3):
PC: box [0]={ 9.73688e+00, 0.0e+00, 0.0e+00}
PC: box [1]={ 3.24470e+00, 9.11683e+00, 0.0e+00}
PC: box [2]={-3.24470e+00, 4.55842e+00, 7.97596e+00}
fshift after SR (27x3):
fshift after SR[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
fshift after SR[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
fshift after SR[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
fshift after SR[3]={ nan, nan, nan}
fshift after SR[4]={ nan, nan, nan}
What am I missing?
Ran Friedman wrote:
Dear all,
I'm trying to run MD with ED sampling. The target structure is a
protein
taken from one simulation, the .tpr file is taken from a different one.
I'm using a subset of the CA atoms to calculate the eigenvectors. The
problem is that the MD run crashes after set-up.
Depending on the machine, it either crashes without any error
message or
complains about "Too many iterations in routine JACOBI".
Any suggestions?
Thanks,
Ran.
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.
--
Bert
__
Bert de Groot, PhD
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
37077 Goettingen, Germany
tel: +49-551-2012308, fax: +49-551-2012302
http://www.mpibpc.mpg.de/groups/de_groot
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Re: [gmx-users] Essential Dynamics Sampling (EDS) MD
Hi Ran,
ok, that's strange. did you try to run it in double prec?
Lars
Ran Friedman wrote:
Dear Lars, GMX users:
It doesn't seem to be the problem, as the initial RMSD from reference
structure =0.16037 nm
I also get:
Large VCM(group rest): nan, nan, nan,
ekin-cm: nan
In the log file.
Ran.
Lars Schaefer wrote:
Dear Ran,
this could mean that you have problems fitting to your reference
structure.
Lars
Ran Friedman wrote:
Dear all,
I'm resending this message (please see below) with some additional
info, hoping that someone can at least point me to what I should check.
I ran the simulation with the -debug flag and got some "nan" values in
mdrun.log:
dekin = nan, ekin = 175815 vcm = ( nan nan nan)
mv = ( nan nan nan)
PC: pres (3x3):
PC: pres[0]={ nan, nan, nan}
PC: pres[1]={ nan, nan, nan}
PC: pres[2]={ nan, nan, nan}
PC: ekin (3x3):
PC: ekin[0]={ nan, nan, nan}
PC: ekin[1]={ nan, nan, nan}
PC: ekin[2]={ nan, nan, nan}
PC: vir (3x3):
PC: vir [0]={ 5.66646e+04, 1.12632e+02, -1.88577e+03}
PC: vir [1]={ 5.10852e+02, 5.71922e+04, 3.69013e+03}
PC: vir [2]={-1.82055e+03, 3.43891e+03, 6.20980e+04}
PC: box (3x3):
PC: box [0]={ 9.73688e+00, 0.0e+00, 0.0e+00}
PC: box [1]={ 3.24470e+00, 9.11683e+00, 0.0e+00}
PC: box [2]={-3.24470e+00, 4.55842e+00, 7.97596e+00}
fshift after SR (27x3):
fshift after SR[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
fshift after SR[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
fshift after SR[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
fshift after SR[3]={ nan, nan, nan}
fshift after SR[4]={ nan, nan, nan}
What am I missing?
Ran Friedman wrote:
Dear all,
I'm trying to run MD with ED sampling. The target structure is a
protein
taken from one simulation, the .tpr file is taken from a different one.
I'm using a subset of the CA atoms to calculate the eigenvectors. The
problem is that the MD run crashes after set-up.
Depending on the machine, it either crashes without any error
message or
complains about "Too many iterations in routine JACOBI".
Any suggestions?
Thanks,
Ran.
___
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Re: [gmx-users] Essential Dynamics Sampling (EDS) MD
Dear Lars, GMX users:
It doesn't seem to be the problem, as the initial RMSD from reference
structure =0.16037 nm
I also get:
Large VCM(group rest): nan, nan, nan,
ekin-cm: nan
In the log file.
Ran.
Lars Schaefer wrote:
> Dear Ran,
> this could mean that you have problems fitting to your reference
> structure.
> Lars
>
> Ran Friedman wrote:
>
>> Dear all,
>>
>> I'm resending this message (please see below) with some additional
>> info, hoping that someone can at least point me to what I should check.
>>
>> I ran the simulation with the -debug flag and got some "nan" values in
>> mdrun.log:
>>
>> dekin = nan, ekin = 175815 vcm = ( nan nan nan)
>> mv = ( nan nan nan)
>> PC: pres (3x3):
>> PC: pres[0]={ nan, nan, nan}
>> PC: pres[1]={ nan, nan, nan}
>> PC: pres[2]={ nan, nan, nan}
>> PC: ekin (3x3):
>> PC: ekin[0]={ nan, nan, nan}
>> PC: ekin[1]={ nan, nan, nan}
>> PC: ekin[2]={ nan, nan, nan}
>> PC: vir (3x3):
>> PC: vir [0]={ 5.66646e+04, 1.12632e+02, -1.88577e+03}
>> PC: vir [1]={ 5.10852e+02, 5.71922e+04, 3.69013e+03}
>> PC: vir [2]={-1.82055e+03, 3.43891e+03, 6.20980e+04}
>> PC: box (3x3):
>> PC: box [0]={ 9.73688e+00, 0.0e+00, 0.0e+00}
>> PC: box [1]={ 3.24470e+00, 9.11683e+00, 0.0e+00}
>> PC: box [2]={-3.24470e+00, 4.55842e+00, 7.97596e+00}
>> fshift after SR (27x3):
>> fshift after SR[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
>> fshift after SR[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
>> fshift after SR[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
>> fshift after SR[3]={ nan, nan, nan}
>> fshift after SR[4]={ nan, nan, nan}
>>
>> What am I missing?
>>
>> Ran Friedman wrote:
>>
>>
>>> Dear all,
>>>
>>> I'm trying to run MD with ED sampling. The target structure is a
>>> protein
>>> taken from one simulation, the .tpr file is taken from a different one.
>>> I'm using a subset of the CA atoms to calculate the eigenvectors. The
>>> problem is that the MD run crashes after set-up.
>>>
>>> Depending on the machine, it either crashes without any error
>>> message or
>>> complains about "Too many iterations in routine JACOBI".
>>>
>>> Any suggestions?
>>>
>>> Thanks,
>>> Ran.
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Re: [gmx-users] Essential Dynamics Sampling (EDS) MD
Dear Ran,
this could mean that you have problems fitting to your reference structure.
Lars
Ran Friedman wrote:
Dear all,
I'm resending this message (please see below) with some additional
info, hoping that someone can at least point me to what I should check.
I ran the simulation with the -debug flag and got some "nan" values in
mdrun.log:
dekin = nan, ekin = 175815 vcm = ( nan nan nan)
mv = ( nan nan nan)
PC: pres (3x3):
PC: pres[0]={ nan, nan, nan}
PC: pres[1]={ nan, nan, nan}
PC: pres[2]={ nan, nan, nan}
PC: ekin (3x3):
PC: ekin[0]={ nan, nan, nan}
PC: ekin[1]={ nan, nan, nan}
PC: ekin[2]={ nan, nan, nan}
PC: vir (3x3):
PC: vir [0]={ 5.66646e+04, 1.12632e+02, -1.88577e+03}
PC: vir [1]={ 5.10852e+02, 5.71922e+04, 3.69013e+03}
PC: vir [2]={-1.82055e+03, 3.43891e+03, 6.20980e+04}
PC: box (3x3):
PC: box [0]={ 9.73688e+00, 0.0e+00, 0.0e+00}
PC: box [1]={ 3.24470e+00, 9.11683e+00, 0.0e+00}
PC: box [2]={-3.24470e+00, 4.55842e+00, 7.97596e+00}
fshift after SR (27x3):
fshift after SR[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
fshift after SR[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
fshift after SR[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
fshift after SR[3]={ nan, nan, nan}
fshift after SR[4]={ nan, nan, nan}
What am I missing?
Ran Friedman wrote:
Dear all,
I'm trying to run MD with ED sampling. The target structure is a protein
taken from one simulation, the .tpr file is taken from a different one.
I'm using a subset of the CA atoms to calculate the eigenvectors. The
problem is that the MD run crashes after set-up.
Depending on the machine, it either crashes without any error message or
complains about "Too many iterations in routine JACOBI".
Any suggestions?
Thanks,
Ran.
___
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[gmx-users] Essential Dynamics Sampling (EDS) MD
Dear all,
I'm resending this message (please see below) with some additional
info, hoping that someone can at least point me to what I should check.
I ran the simulation with the -debug flag and got some "nan" values in
mdrun.log:
dekin = nan, ekin = 175815 vcm = ( nan nan nan)
mv = ( nan nan nan)
PC: pres (3x3):
PC: pres[0]={ nan, nan, nan}
PC: pres[1]={ nan, nan, nan}
PC: pres[2]={ nan, nan, nan}
PC: ekin (3x3):
PC: ekin[0]={ nan, nan, nan}
PC: ekin[1]={ nan, nan, nan}
PC: ekin[2]={ nan, nan, nan}
PC: vir (3x3):
PC: vir [0]={ 5.66646e+04, 1.12632e+02, -1.88577e+03}
PC: vir [1]={ 5.10852e+02, 5.71922e+04, 3.69013e+03}
PC: vir [2]={-1.82055e+03, 3.43891e+03, 6.20980e+04}
PC: box (3x3):
PC: box [0]={ 9.73688e+00, 0.0e+00, 0.0e+00}
PC: box [1]={ 3.24470e+00, 9.11683e+00, 0.0e+00}
PC: box [2]={-3.24470e+00, 4.55842e+00, 7.97596e+00}
fshift after SR (27x3):
fshift after SR[0]={ 0.0e+00, 0.0e+00, 0.0e+00}
fshift after SR[1]={ 0.0e+00, 0.0e+00, 0.0e+00}
fshift after SR[2]={ 0.0e+00, 0.0e+00, 0.0e+00}
fshift after SR[3]={ nan, nan, nan}
fshift after SR[4]={ nan, nan, nan}
What am I missing?
Ran Friedman wrote:
> Dear all,
>
> I'm trying to run MD with ED sampling. The target structure is a protein
> taken from one simulation, the .tpr file is taken from a different one.
> I'm using a subset of the CA atoms to calculate the eigenvectors. The
> problem is that the MD run crashes after set-up.
>
> Depending on the machine, it either crashes without any error message or
> complains about "Too many iterations in routine JACOBI".
>
> Any suggestions?
>
> Thanks,
> Ran.
>
>
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[gmx-users] Essential Dynamics Sampling (EDS) MD
Dear all, I'm trying to run MD with ED sampling. The target structure is a protein taken from one simulation, the .tpr file is taken from a different one. I'm using a subset of the CA atoms to calculate the eigenvectors. The problem is that the MD run crashes after set-up. Depending on the machine, it either crashes without any error message or complains about "Too many iterations in routine JACOBI". Any suggestions? Thanks, Ran. -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: [EMAIL PROTECTED] Skype: ran.friedman -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
