Dear Amber community,
sorry if this topic has been already posted. Before writing I checked
extensively the mailing list and it seems this option is not active yet,
but I was wondering if there was some last minute news concerning this
point, even at the level of developing codes.
Namely, I was wondering if there is any way in AMBER14 of using a
generalized restraint (namely restraining the difference between two
distances, each involving centers of mass of groups of atoms) using pmemd
in place of sander.
I have seen that the distance between centers of mass has been implemented (
http://ambermd.org/bugfixes/14.0/update.10), but as far as I can see from
the manuals, there is no way of implementing such generalized coordinates
by using the GPU version of the code.
I understood that with the "old" syntax one should use something like the
following example, which indeed seems to work properly for my system (or
better, sander runs...):
&rst
iat= -1, -1, -1, -1,
iresid=0,
igr1=47555,47556,47557,0,
igr2=18543,18560,18581,18591,0,
igr3=47555,47556,47557,0,
igr4=18543,18560,18581,0,
grnam1(1)='O2',grnam1(2)='C2',grnam1(3)='C3',
grnam2(1)='CA',grnam2(2)='CA',grnam2(3)='CA',grnam2(4)='CA',
grnam3(1)='O2',grnam3(2)='C2',grnam3(3)='C3',
grnam4(1)='CA',grnam4(2)='CA',grnam4(3)='CA',
r1=0.0, r2=37.43418, r3=37.43418, r4=100.0, rk2=10.0, rk3=10.0,
rstwt=1.0,-1.0
/
The same input clearly does not work with pmemd (because of rstwt option
not implemented in plumed, I understood), with error:
At line 1015 of file nmr_calls.F90 (unit = 33, file = 'us_window9.RST_old')
Fortran runtime error: Bad data for namelist object igr2
Thanks in advance for your help!
Best Regards,
Attilio
--
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Attilio Vittorio Vargiu, PhD
Assistant Professor at Department of Physics, University of Cagliari
Cittadella Universitaria S.P. Monserrato-Sestu Km 0.700
09042 Monserrato (CA), Italy
e-mail1: vargiu.dsf.unica.it
e-mail2: attilio.vargiu.gmail.com
web: http://people.unica.it/attiliovargiu
Phone: +390706754911
Fax: +390706753191
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Received on Tue Mar 24 2015 - 07:30:03 PDT
