[gmx-users] Essential Dynamics Sampling (EDS) MD

Bert de Groot bgroot at gwdg.de
Fri Jan 12 12:42:48 CET 2007

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

> 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
>>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
>>>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,  0.00000e+00,  0.00000e+00}
>>>  PC: box [    1]={ 3.24470e+00,  9.11683e+00,  0.00000e+00}
>>>  PC: box [    2]={-3.24470e+00,  4.55842e+00,  7.97596e+00}
>>>fshift after SR (27x3):
>>>  fshift after SR[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>>>  fshift after SR[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
>>>  fshift after SR[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+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
>>>>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?
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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

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