Please anyone respond
*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*
On Mon, 14 Jul, 2025, 10:04 am Dulal Mondal, <
babunmondal.chem.kgpian.iitkgp.ac.in> wrote:
> Sorry for the late reply. Thank you for your reply. The cv files looks
> like.
> cv_file
> &colvar
> cv_type = 'ANGLE'
> cv_ni = 3, cv_i =82,83,84
> cv_min = 1.8
> cv_max = 3.14159
> resolution = 0.05
>
> /
>
> &colvar
> cv_type = 'DISTANCE'
> cv_ni = 2, cv_i = 83,11423
> cv_min = -1.0
> cv_max = 3.5
> resolution = 0.5
>
> /
>
> &colvar
> cv_type = 'DISTANCE'
> cv_ni = 2, cv_i = 83,47576
> cv_min = -1.0
> cv_max = 3.5
> resolution = 0.5
>
> /
>
>
> &colvar
> cv_type = 'TORSION'
> cv_ni = 4, cv_i = 991,993,995,998
> cv_min = -3.14
> cv_max = 3.14
> resolution = 0.1
> /
>
>
>
>
> On Sun, Jul 13, 2025 at 10:37 AM Feng Pan <fpan3.alumni.ncsu.edu> wrote:
>
>> Hi, Dulal Mondal
>>
>> What is your collective variable? can you show your cv.dat file
>>
>>
>> On Sat, Jul 12, 2025 at 10:22 AM Dulal Mondal via AMBER <
>> amber.ambermd.org> wrote:
>>
>>> Dear Experts,
>>>
>>> My input file for abmd is like below:
>>>
>>> infe=1,
>>> /
>>>
>>> &abmd
>>> mode = 'FLOODING'
>>> timescale = 10
>>> umbrella_file = 'umbrella1.nc'
>>> monitor_file = 'abmd1.dat'
>>> monitor_freq = 10
>>> cv_file = 'cv.dat'
>>> /
>>> *But in the abmd.dat file or in the mdout file bais value is zero. *
>>>
>>>
>>> 1-4 NB = 916.1329 1-4 EEL = 13018.3691 VDWAALS =
>>> 31294.6763
>>> EELEC = -250037.8763 EHBOND = 0.0000 RESTRAINT =
>>> 0.0000
>>>
>>> ------------------------------------------------------------------------------
>>>
>>> NFE restraints: SMD : 0.000 PMD : 0.000 * ABMD :
>>> 0.000*
>>> BBMD : 0.000 STSM : 0.000
>>>
>>> ===============================================================================
>>>
>>> NSTEP = 9985000 TIME(PS) = 9985.000 TEMP(K) = 301.26 PRESS =
>>> 0.0
>>> Etot = -120118.0596 EKtot = 47654.7578 EPtot =
>>> -167772.8174
>>>
>>> What wrongs occur in the simulation?
>>> --
>>> *With regards,*
>>> *Dulal Mondal,*
>>> *Research Scholar,*
>>> *Department of Chemistry,*
>>> *IIT Kharagpur, Kharagpur 721302.*
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>> --
>> Feng Pan
>> Senior Research Scientist
>> Email: fpan3.ncsu.gmail.com; fpan3.alumni.ncsu.edu
>> *(The email fpan3.ncsu.edu <fpan3.ncsu.edu> will be disabled soon, please
>> use fpan3.ncsu.gmail.com <fpan3.ncsu.gmail.com> or fpan3.alumni.ncsu.edu
>> <fpan3.alumni.ncsu.edu> instead)*
>>
>
>
> --
> *With regards,*
> *Dulal Mondal,*
> *Research Scholar,*
> *Department of Chemistry,*
> *IIT Kharagpur, Kharagpur 721302.*
>
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Received on Tue Jul 15 2025 - 06:00:02 PDT
