From: Hannah Scott (hrs00003_at_mix.wvu.edu)
Date: Mon Dec 27 2021 - 09:46:23 CST
Just updating this to say that I have not found a solution to this problem. Does anyone have any suggestions?
> On Dec 9, 2021, at 7:43 PM, ROPÓN-PALACIOS G. <biodano.geo_at_gmail.com> wrote:
>
> Try use Occupancy column and not beta
>
> In contrast with guide only atoms tagged Eith no-zero values into beta column are used as pulling atoms.
>
> https://www.ks.uiuc.edu/Research/namd/2.9/ug/node48.html
>
> Enviado desde mi iPhone
>
>> El 9 dic. 2021, a la(s) 3:41 p. m., Hannah Scott <hrs00003_at_mix.wvu.edu> escribió:
>>
>>
>> I am seeing an unusually high force being applied in the wrong direction when applying constant velocity steered MD to my system. For this simulation I am applying SMD to a single alpha-carbon in a helical peptide and pulling along the -z axis in an attempt to simulate insertion into a membrane bilayer with a 1 fs timestep.
>>
>> When visualizing my system, I see that the peptide is being pulled in the +z direction instead. The SMD output shows that the initial force applied is very large. What could be causing this and what do you recommend I try?
>>
>> The following are the parameters I have set for the SMD simulation as well as the output:
>>
>> SMD on
>> SMDFile ../current-parameters/rev-smd.ref ;# this is the pbd file with b-column needs remade with different systems
>> SMDk 10 ;#adjusted to pull on termius of phlip
>> SMDVel .00001 ;# 10 A/ns = .01 A/ps = .00001 A/fs
>> SMDDir 0 0 -1
>> SMDOutputFreq 100
>>
>>
>> SMD 0 5.801 -4.258 27.644 0 -0 27336.5
>> SMD 100 6.09131 -4.67441 31.9466 0 -0 24346.4
>> SMD 200 6.91383 -3.83161 34.0325 0 -0 22896.4
>> SMD 300 7.37256 -3.92352 36.4932 0 -0 21186.1
>> SMD 400 7.21118 -4.2608 39.8742 0 -0 18836.3
>> SMD 500 6.8234 -3.46171 43.0824 0 -0 16606.6
>> SMD 600 6.92947 -2.77978 46.19 0 -0 14446.8
>> SMD 700 7.27499 -2.5372 48.6056 0 -0 12767.7
>> SMD 800 8.21247 -2.39816 50.8552 0 -0 11204
>> SMD 900 8.02797 -1.72661 53.5881 0 -0 9304.52
>> SMD 1000 7.32698 -1.27389 55.6482 0 -0 7872.5
>>
>>
>>
>> Thank you in advance,
>> Hannah
This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:12 CST