Re: Re: I don't have any eabf output file.

From: philippe Bourly (philippe.bourly20_at_gmail.com)
Date: Tue Jul 25 2017 - 07:23:34 CDT

Thank you Haohao.

That was my mistake. I have one more question: When I had the option
‘hidejacobian on’ on my .in file, my number of sample in the count file is
close to 0. Do you know why?

Philippe

On Tue, Jul 25, 2017 at 1:20 PM, Haohao <fhh2626_at_gmail.com> wrote:

> Hi,
>
> Did you set scriptcolvarforces on in your .in file?
>
> Haohao
>
>
>
>
>
> On 2017-07-25 18:20 , philippe Bourly <philippe.bourly20_at_gmail.com>
> Wrote:
>
> Hi,
>
> No, I don't have those files in my output folder.
>
> Philippe
>
>
>
> On Tue, Jul 25, 2017 at 12:06 PM, <yjcoshc_at_gmail.com> wrote:
>
>> Hi,
>>
>> Do you have sod2_test.eabf.count and sod2_test.eabf.grad in your output
>> folder?
>>
>> 在 2017年07月22日 02:46, philippe Bourly 写道:
>>
>> Hello !
>>
>>
>>
>> I am trying to run an eabf simulation with the RMSD as the collective
>> variable. My calculation is running but I don’t have any output files for
>> the eabf.
>>
>>
>>
>> In my configuration file I added:
>>
>>
>>
>> source ./scripts/eabf.tcl
>>
>> set eabf_inputname 0
>>
>> set eabf_outputname output/sod2_test.eabf
>>
>> set eabf_temperature 300
>>
>> set eabf_outputfreq 10000
>>
>>
>>
>> But I don’t have any file named sod2_test.eabf in my output folder and I
>> don’t have any errors too. Does anybody know why ?
>>
>>
>>
>>
>>
>> Below is my colvar configuration file (Does this look correct for you?):
>>
>>
>> Colvarstrajfrequency 200
>>
>> Colvarsrestartfrequency 200
>>
>>
>>
>>
>>
>> colvar {
>>
>> name rmsd_sod
>>
>> width 0.1
>>
>>
>>
>> lowerboundary 1.00
>>
>> upperboundary 2.00
>>
>> lowerwallconstant 100.00
>>
>> upperwallconstant 100.00
>>
>> extendedLagrangian on
>>
>> extendedFluctuation 0.1
>>
>>
>>
>>
>>
>> rmsd {
>>
>> atoms {
>>
>> atomsFile ./reference.pdb
>>
>> atomsCol B
>>
>> atomsColValue 2.0
>>
>> }
>>
>> refpositionsfile ./reference.pdb
>>
>> }
>>
>> }
>>
>>
>>
>> }
>>
>>
>>
>> abf {
>>
>> colvars rmsd_sod
>>
>> FullSamples 5000
>>
>> historyfreq 10000
>>
>> }
>>
>>
>>
>> Thanks,
>>
>> Philippe
>>
>>
>>
>

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