[AMBER] About generalized restraints in AMBER14 with GPU support

From: Attilio Vittorio Vargiu <vargiu.dsf.unica.it>
Date: Tue, 24 Mar 2015 15:29:28 +0100

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...):

 iat= -1, -1, -1, -1,
 r1=0.0, r2=37.43418, r3=37.43418, r4=100.0, rk2=10.0, rk3=10.0,

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 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
AMBER mailing list
Received on Tue Mar 24 2015 - 07:30:03 PDT
Custom Search