Hi Dr. Case,
Thanks for the comments. The issue with rising energies seems to be entirely because I accidentally used a submission script for pmemd.cuda; I know I’m not suppose to use GPUs for minimization! On a CPU, the energies are nicely becoming more negative with the input file at the end of this message.
However, a few questions remain.
1) I get the following error message with ntmin=1
ERROR: Minimizations with ifsc=1 require the steepest descent algorithm.
Set ntmin to 2 and restart.
I suppose I could minimize the lambda end points with ntmin=1 and the prmtop not set up for TI yet. Then, re-build the system with TLEaP and ParmEd to setup the prmtop for TI. Does this seem better than just doing steepest descent (ntmin=2) with the prmtop setup for TI?
Also, what should I look for in the output to make sure the TI calculations make sense? For example, I’m running minimizations with lambda = 0.0, 0.5, and 1.0. I see that DV/DL (at the current step) for these minimizations is respectively +481, 30, -428, which seems roughly to make sense—I realize I should really compare averages. What else should I check?
For example, is there a way to check that the charges on the TI but non-softcore atoms are being scaled correctly?
Input file:
minimisation
&cntrl
imin=1, ! Perform an energy minimization
ntb=1, ! Boundaries (=1, constant volume)
cut=10.0, ! Cutoff
ntmin=2, ! Method of minimization
ncyc=10000, ! Number of steepest descent cycles
maxcyc=50000, ! Maximum number of minimization cycles
igb=0, ! GB model (=0, explicit solvent)
ntr=1, ! Turn on positional restraints
restraintmask='.CA,C,O,N|(:HEH,PRN)@FE,NA,NB,NC,ND,C3D,C2A,C3B,C2C,CA,CB',
restraint_wt=10.0, ! 10 kcal/mol.A**2 restraint force constant
icfe = 1, !free energy calculations
ifsc = 1, !1 SC potentials are used
clambda = 0.50, !Zero corresponds to the unperturbed Hamiltonian V0. l=1 corresponds to the perturbed Hamiltonian V1
scalpha = 0.5, ! default value is 0.5
scbeta = 12.0, ! Default value is 12A2
logdvdl = 0, !If set to .ne. 0,calculated during every step of the run will be printed out at the end of the simulation
klambda = 1, !
timask1='.3630,3631,3632,3633,3634,3635,3636,3637,3638,3639,3640,3641,3642,3643,3644,8025,8026,8027,8028,8029,8030,8031,8032,8033,8034,8035,8036,8037,8038,8039,8040,8041,8042,8043,8044,8045,8046',
timask2='.8791,8792,8793,8794,8795,8796,8797,8798,8799,8800,8801,8802,8803,8804,8805,8806,8807,8808,8809,8810,8811,8812,8813,8814,8815,8816,8817,8818,8819,8820,8821,8822,8823,8824,8825,8826,8827',
scmask1='.3642,3643,3644,8037,8038,8039,8040,8041,8042,8043,8044,8045,8046',
scmask2='.8803,8804,8805,8806,8807,8808,8809,8810,8811,8812,8825,8826,8827',
/
Best,
Matthew
> On Sep 2, 2022, at 3:24 PM, David Case via AMBER <amber.ambermd.org> wrote:
>
> *Message sent from a system outside of UConn.*
>
>
>> ntr = 1, restraint_wt = 100.00,
>> restraintmask='!:WAT',
>
> This is very high restraint weight; are you sure that you don't want any
> of the waters to move?
>
> Sorry: I missed the "!" character. Still, if you want to minimize waters, be sure that SHAKE is turned on (ntc=ntf=2).
> [Not setting this can sometimes, but not aways, cause problems.]
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=05%7C01%7C%7C83b2b98faea54e4b509808da8d213fec%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637977471195738782%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=46qj2pJwT0yUQSZU%2Fz3y3dRdOmmRygyF9%2F9bZb0OZyk%3D&reserved=0
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=05%7C01%7C%7C83b2b98faea54e4b509808da8d213fec%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637977471195738782%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=46qj2pJwT0yUQSZU%2Fz3y3dRdOmmRygyF9%2F9bZb0OZyk%3D&reserved=0
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 02 2022 - 21:00:06 PDT
