[gmx-users] Essential Dynamics Sampling (EDS) MD
Ran Friedman
r.friedman at bioc.unizh.ch
Thu Jan 11 15:48:30 CET 2007
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, 0.00000e+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
>>> 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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