Re: inputPrefix in ABF

From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Thu Aug 16 2012 - 04:02:32 CDT

Thank you Jerome,

In previous mail I sent colvars configuration file with included
'inputPrefix' option, still NAMD didn't recognize it properly, and in
this way I am unable to merge two ABF trajectories. Once again colvar
configuration is attached. In the same directory there are
24diiPr-dmso-sech-md3.grad, 24diiPr-dmso-sech-md3.count,
24diiPr-dmso-sech-md5.grad, 24diiPr-dmso-sech-md5.count - ABF output
from two subsequent runs which should be merged.

Branko

On 8/16/2012 8:51 AM, Jérôme Hénin wrote:
> Hi Branko,
>
> inputPrefix is an ABF option. Its place is in the ABF block, in the
> colvars config.
>
> Jerome
>
>
> On 14 August 2012 19:04, Branko<bdrakuli_at_chem.bg.ac.rs> wrote:
>> Hi,
>>
>> I try to merge two ABF outputs (grad and count), obtained by consequent runs
>> by using inputPrefix, but NAMD stoped with the message at the end of the
>> out file:
>>
>> 'Error: keyword "inputprefix" is not supported, or not recognized in this
>> context.'
>>
>> I initialized third run, as the continuation of the previous two sequential
>> runs, and this calculation should last only 10 steps, just to merge grad and
>> count file of colvars (i.e. ABF). There is no other errors in input files or
>> configuration. Colvars input is given below, any advice is appreciated
>>
>> Branko
>>
>> colvarsTrajFrequency 100
>> colvarsRestartFrequency 10000
>> analysis on
>> inputPrefix 24diiPr-dmso-sech-md3 #-this is prefix from run I (from #
>> not included in original input)
>> 24diiPr-dmso-sech-md5 #-this is prefix from run II
>> (from # not included in original input)
>>
>>
>> colvar {
>>
>> name d
>>
>> lowerBoundary 2.80
>> upperBoundary 10.20
>> width 0.01
>>
>> distance {
>> group1 {
>> atomnumbers 1 3 5
>> }
>> group2 {
>> atomnumbers 16 17 18
>> }
>> }
>> }
>> colvar {
>> name gyration
>> lowerBoundary 2.80
>> upperBoundary 4.90
>> width 0.01
>>
>> gyration {
>> atoms {
>> atomNumbers 7 8 9 10 11 12 13 14 15 19 20 21 22 23 24
>> }
>> }
>> }
>>
>> abf {
>> colvars d gyration
>> fullSamples 500
>> hideJacobian no
>> outputFreq 1000
>> applyBias yes
>> }
>>
>>
>>
>>
>>
>>
>>
>>
>>
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