Replying to David here as I receive digest mail:
*"No: it is telling you to set nmropt=1, and not to include a reference to
a DISANG file in the redirection section. If you don't have any
internal restraints, you will have no &rst namelists, and hence no need for
a DISANG **file"*.
Apologies, I misunderstood the term "internal" as I am restraining a
distance between molecules.
*"Step 0 may indeed be special. Try this: run a 1 step MD with no
restraints; then do a restart calculation from that, using the restraints.
That will start at step 1, and may do what you want."*
The restraints are applied from Step 0 and onwards, whereas I want them to
ramp up slowly from step 100,000 onwards.
*I'm a little confused, however, since the REST weight change command
doesn't **make any sense if you don't have distance (or other NMR-like)
restraints*.
I'll be clearer on what I need: distance restraints and I want them to ramp
using weights from 0.00001 to 1 over time. How would I do this? I created
my DISANG file using makeDIST_RST and an 8 column input file. Here is a
part of the DISANG file I am redirecting to:
# 534 VAL O 781 0SA N5 1.8 3.0
&rst
ixpk= 0, nxpk= 0, iat=8163,12217, r1= 1.30, r2= 1.80, r3= 3.00, r4= 3.50,
rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
&end
I discovered I can turn on/off restaints at a particular time like this:
&rst
ixpk= 0, nxpk= 0, iat=8163,12217, nstep1=0, nstep2=900, r1= 1.30, r2=
1.80, r3= 3.00, r4= 3.50,
rk2=0.0, rk3=0.0, ir6=1, ialtd=0,
&end
&rst
ixpk= 0, nxpk= 0, iat=8163,12217, nstep1=901, nstep2=10000, ifvari=1, r1=
1.30, r2= 1.80, r3= 3.00, r4= 3.50,
rk2=20.0, rk3=20.0, &end
However I can't figure out how to ramp the weights over time.
Oliver
On Fri, Jul 10, 2015 at 11:02 AM, Oliver Grant <olivercgrant.gmail.com>
wrote:
> Hi all,
>
> I'm confused by the instructions in section 23.1 of the amber14 manual. I
> would like to include weight changes to my NMR distance restraints but the
> weight changes are not being applied when I run the simulation. The manual
> states:
>
> *If you wish to include weight changes but have no internal constraints,
> set nmropt=1, but do not include a*
> *DISANG line in the file redirection section. (Note that, unlike earlier
> versions of Amber, the &rst namelists must*
> *be in the DISANG file, and not in the mdin file.)*
>
> It's telling me to put the &rst namelists in the DISANG file, but don't
> redirect to the DISANG file.
>
> I want weight changes and have no internal constraints. But if I can't
> redirect to my DISANG file and can't include the &rst namelists in the mdin
> file, how do I use weight changes? This reads very strange. I've tried
> including a redirect to my DISANG and including the namelists in the mdin
> file. I can get the restraints applied, but not the weights. The outfile is
> misleading. It prints the weight changes I want, but in step 0 they are not
> applied.
>
> Begin reading energy term weight changes/NMR restraints
> WEIGHT CHANGES:
> TEMP0 1 900 5.000000 25.000000 0 0
> TEMP0 901 1000 25.000000 25.000000 0 0
> REST 0 100 0.000000 0.000000 0 0
> REST 101 1000 0.010000 1.000000 0 0
>
> RESTRAINTS:
> No valid redirection requests found
> Number of restraints read = 7
>
> Done reading weight changes/NMR restraints
>
>
>
> Number of triangulated 3-point waters found: 0
> | Dynamic Memory, Types Used:
> | Reals 375537
> | Integers 1264979
>
> | GPU memory information (estimate):
> | KB of GPU memory in use: 46289
> | KB of CPU memory in use: 9521
>
>
> --------------------------------------------------------------------------------
> 4. RESULTS
>
> --------------------------------------------------------------------------------
>
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 6.04 PRESS =
> 0.0
> Etot = -19182.6968 EKtot = 183.9096 EPtot =
> -19366.6064
> BOND = 410.8933 ANGLE = 1504.4187 DIHED =
> 8324.6308
> 1-4 NB = 2507.8961 1-4 EEL = 39306.9026 VDWAALS =
> -7029.6448
> EELEC = -57726.7863 EGB = -8926.8055 RESTRAINT =
> 2261.8888
> EAMBER (non-restraint) = -21628.4951
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 2261.889 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
>
>
> Oliver
>
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Received on Tue Jul 14 2015 - 07:30:03 PDT
