On 11/8/17 8:59 PM, Amali Guruge wrote:
Dear Dr. Justin,
Thank you very much for the reply. If I keep the 0.005 as the time step,
what steps should be followed in-order to avoid the LINCS warnings?
Appreciate if you can comment on this.
I already suggested the only two appropriate methods for doing this (see
below).
-Justin
Thank you.
On Thu, Nov 9, 2017 at 12:46 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 11/8/17 8:45 PM, Amali Guruge wrote:
Dear Gromacs users,
I did energy minimization step and started the equilibration run. However,
when I changed the time step 0.002 to to 0.005, it gave an error; Too many
LINCS warnings. What could be the reason for this? The simulation was
worked without an error until I changed the time step. Appreciate if
anyone
can give me a solution.
A 5-fs timestep is only stable is using some topological modification like
virtual sites and/or hydrogen mass repartitioning. Generally, a 2-fs
timestep is an upper limit without such tricks.
-Justin
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Virginia Tech Department of Biochemistry
303 Engel Hall
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Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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