On 11/5/19 7:53 PM, Dave M wrote:
Hi Justin,
Will appreciate any suggestions about the error am getting with
distance_restraints.
Aside from using the pull code rather than this approach, I have no
other suggestions.
-Justin
Thanks.
regards,
Dave
On Thu, Oct 31, 2019 at 1:39 AM Dave M <dave.gro...@gmail.com> wrote:
Hi Justin,
Thanks, not sure [distance_restraints] also does not work for me. Though
pull code works (like shared by other user Mustafa in recent discussions).
My top files contain this:
[ intermolecular_interactions ]
[ distance_restraints ]
; ai aj type index type’ low up1 up2 fac
1 155 1 0 1 0.0 0.3 0.4 1.0
I get this error:
NMR distance restraints with multiple copies of the same molecule are
currently only supported with ensemble averaging. If you just want to
restrain
distances between atom pairs using a flat-bottomed potential, use a
restraint
potential (bonds type 10) instead.
I do not have multiple copies of the same molecule (except water
molecules!) and the atom numbers here belong to two different molecules. I
also tried using type' = 2 but still error remains the same. Would have
been great if distance_restraints work as it seems to be bit cleaner way
than modifying a pull code. I want to keep number of small molecules near
to a rod like bigger molecule; just like beads on a string. So
distance_restraints or something similar will be great.
Dave
On Tue, Oct 29, 2019 at 5:45 AM Justin Lemkul <jalem...@vt.edu> wrote:
On 10/28/19 6:21 PM, Dave M wrote:
Hi Justin,
Thanks for your reply but am getting error suggesting a intermolecular
chemical bond is not allowed:
Program: gmx grompp, version 2016.4
Source file: src/gromacs/gmxpreprocess/convparm.cpp (line 649)
Fatal error:
The intermolecular_interaction can not contain chemically bonding
interactions
[ molecules ]
; name number
molA 1
molB 1
W 2420
[intermolecular_interactions]
[ bonds ]
1 158 1 0.4 2000
This is coarse-grained model and as a simple test I used global atom
numbers between two water single particles (intermolecular) but I get
the
same error.
In that case, use a [distance_restraints] directive under
[intermolecular_interactions] (though this will limit your domain
decomposition setup) or use the pull code to maintain a restraint rather
than messing with the topology.
-Justin
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==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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