Dear Dave,
I have followed your suggestion, and after 10 ps, I dont see anything
strange happening. Namely, everything works fine. The md.in file I use is
the following:
-------------------------- md.in ---------------------------------------
100000 fs simulation
&cntrl
imin=0,
ntx=5,irest=1,
ntpr=50,ntwr=50,ntwx=100,
ntc=2,ntf=1,ntb=1,cut=10,
noshakemask = '.%DH | (.%H & !.H1)',
igb=0,
ntr=0,
nstlim=100000,dt=0.001,nscm=5000,nrespa=1,
ntt=3,gamma_ln=1,tempi=300,temp0=300,ig=233,
ntp=0,taup=2.0,pres0=1,
icfe=2,klambda=6,clambda=$lambda
-------------------------------------------------------------------------
Here, $lambda = 0.5 (in the test I have been doing). It works with icfe=1.
I have done something else, too, but that did not work. I changed all of
the DH type to HZ type (which is defined in the parm.99 too). In the
frcmod file, I entered the dummy atom parameters to HZ. The reason why I
did this is to see if SHAKE is constraining all of the H? type atoms. And
it did not work. I dont know why this happened. Anyways, noshakemask is a
very nice solution. Thanks.
Best,
On Fri, 17 Mar 2006, David A. Case wrote:
> On Thu, Mar 16, 2006, Ilyas Yildirim wrote:
> >
> > 4. When SHAKE is turned on (see ./ntc_2_ntf_2_icfe_1_ntb_1), the
system
> > blows up.
>
> Have you read note (5) on p. 156 of the Users' Manual. Amber right now
does
> a check that the *number* of shaken bonds is the same in both states,
but it
> does not really check that the list of shaken bonds is identical (with
> identical equilibrium bond lengths.) Patches to further validate the
input
> files would be welcome.
>
> >
> > The reason why it does not work when SHAKE is turned ON is because of
the
> > DH bonds. I think SHAKE is just constraining the H-bonds, not
DH-bonds.
> > DH-bonds are also like H-bonds, but the atom type for these dummy
atoms
> > are DH, not H or H?.
>
> It uses the element type in LEaP (I think). So you would have to tell
LEaP
> that your dummy atoms are hydrogens. But using noshakemask would be a
better
> solution. It would be great if you could try this (add noshakemask,
with
> ntc=2) since it has not been tested very much.
>
> ...thanks!...dave
>
>
--
Ilyas Yildirim
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Received on Wed Apr 05 2006 - 23:49:37 PDT
