Dear Feng,
Thanks a lot for your answer.
I’ve tried what you've suggested following the example in the amber documentation and it’s working now!
This is how I've modified the input for the A10 Tutorial and that it’s now working with the latest version of Amber 16 (in case someone would encounter the same issue).
Malonaldehyde: NCSU steered MD: LCOD rxn coord
&cntrl
imin = 0,
irest = 1,
ntx = 5,
ntb = 0,
cut = 999.0,
tempi = 300.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1.0,
ntf = 2, ntc = 2, tol = 0.00001,
dt = 0.0005,
ntpr = 50, ntwr=100, ntwx = 100,
nstlim = 100000,
ifqnt = 1, infe=1
/
&qmmm
qmmask=':*',
qmcharge=0,
qm_theory='DFTB',
qmshake=0,
writepdb=1,
/
&smd
output_file = 'smd.txt'
output_freq = 1000
cv_file='cv.in'
/
And here is the cv.in file:
&colvar
cv_type = 'LCOD'
cv_ni=4, cv_i = 8,9,7,9,
cv_nr=2, cv_r = 1.0,-1.0,
npath =2, path = 0.7,-0.7,
nharm=1, harm = 1000.0
/
Sincere regards,
Ruth
> On 17 Nov 2016, at 18:03, Feng Pan <fpan3.ncsu.edu> wrote:
>
> Hi, Ruth
>
> Are you using the latest Amber16 with newest updates. If so, the format to
> apply SMD has been changed to &namelist style, also the variable infe=1
> needs to be defined inside &cntrl
>
> you can check this manual for details
> http://ambermd.org/doc12/nfe.pdf
>
> Best
> Feng
>
> On Thu, Nov 17, 2016 at 5:45 AM, Ruth Helena Tichauer <rhtichau.laas.fr>
> wrote:
>
>> Dear Amber users,
>>
>> I’ve been trying to run SMD of a protein with its ligand in explicit
>> solvent using as variable type the Linear Combination Of Distances.
>> Although the run has finished with no error messages, the output_file
>> (nat1_smd.txt) is not written. Here is my input file:
>>
>> NCSU steered MD : LCOD rxn coord
>> &cntrl
>> imin=0,
>> irest=1, ntx=5,
>> ntb=2, pres0=1.0, ntp=1, taup=1.0,
>> cut=12.0,
>> tempi=300.0, temp0=300.0,
>> ntt=3, gamma_ln=2.0, ig=-1,
>> nstlim=50000, dt=0.001,
>> ntpr=25, ntwx=50, ntwr=100, ioutfm=1,
>> ntc=2, ntf=2,
>> noshakemask = '.2828-2851,2931-2936,5394-5396',
>> ntr=1,
>> restraintmask = ':170,185,.CA,C,N',
>> restraint_wt=5.0,
>> ifqnt=1,
>> /
>> &qmmm
>> qmmask = ':179,186-187,1007',
>> qmcharge=-1,
>> qm_theory='PM3',
>> qmshake=0,
>> qmcut=8.0,
>> /
>>
>> ncsu_smd
>> output_file = ‘nat1_smd.txt'
>> output_freq = 50
>>
>> variable
>> type = LCOD
>> i = (5394,5395,2649,5395)
>> r = (1.0,-1.0)
>> path = (0.9,-0.9)
>> harm = (1000.0)
>> end variable
>>
>> end ncsu_smd
>>
>> To check out, I’ve tried to do the same kind of simulation following the
>> corresponding tutorial (A10) and again, although the run finishes smoothly,
>> with no errors and an effective proton transfer, the output_file (smd.txt)
>> is not written. This is the command I used to launch the calculation using
>> the provided files:
>>
>> $AMBERHOME/bin/sander -i mdin -p mr.top -c mr_eq.rst -o mr_pd.out -r
>> mr_pd.rst -x mr_pd.nc &
>>
>> I wonder if I’m missing something from the tutorial.
>>
>> I’m using Ambertools and Amber 16.
>>
>> Thank you for any suggestion on this matter,
>>
>> Sincerely,
>>
>> Ruth
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Feng Pan
> Ph.D. Candidate
> North Carolina State University
> Department of Physics
> Email: fpan3.ncsu.edu
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
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>
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Received on Fri Nov 18 2016 - 07:30:03 PST
