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 Sun Jul 13 2025 - 22:00:02 PDT
