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<p>Hi, sorry if I bother you again with the velocity verlet
algorithm, but I have another question, in the Gromacs Manual
for the Velocity verlet algorithm for the position is written
that r (t + deltaT) is equal to:<img
src="cid:part1.D73502DA.31673C0B@yahoo.it" alt="" height="51"
width="297"></p>
<p>But if I look in the gromacs code, in the update.cpp file I see
that the position for the verlet algorithm the update of the
positions is due as:</p>
<p> <br>
</p>
<img src="cid:part2.9B966067.0A9ED8A8@yahoo.it" alt="" height="16"
width="413"><br>
and I don't see the therm of the Force multiplied for
deltaT^2/2*m, is because in the code the therm v[n] is interpreted
as v(t + delta)?<br>
thanks in advance<br>
Best Regards <br>
Elena della Valle<br>
<br>
<br>
<br>
<div class="moz-cite-prefix">Il 06/10/2016 12:03, Berk Hess ha
scritto:<br>
</div>
<blockquote cite="mid:0cbcd7d5-e229-3a30-1996-5259148ce698@kth.se"
type="cite">
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<div class="moz-cite-prefix">do_update_vv_vel() is called twice
during each step at different points. Thus the updates for
F(t) and F(t+dt) are done separately.<br>
<br>
Berk<br>
<br>
On 2016-10-06 11:53, Elena della Valle wrote:<br>
</div>
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cite="mid:5fe1b537-d484-5e5a-7b25-295cfd941e94@yahoo.it"
type="cite">
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<p>The question is that on the gromacs manual I read that the
verlet algorithm for the velocity corresponds to <img
src="cid:part3.30636571.8E827338@yahoo.it" alt=""
height="36" width="268">, now in the gromacs code in the
verlet part I don't find the corresponds for the term
[1/2*(∆t/m)* F(t + ∆t)], is not implemented?</p>
<p>Sorry if I'm not so clear <br>
</p>
<p>Thanks <br>
</p>
<p>Elena della Valle<br>
</p>
<br>
<div class="moz-cite-prefix">Il 06/10/2016 11:39, Berk Hess ha
scritto:<br>
</div>
<blockquote
cite="mid:5b7f7136-f5dc-ec57-bb5f-4897611299ce@kth.se"
type="cite">I don't understand our question. <br>
accel[ga] is a fixed acceleration per atom for
non-equilibrium dynamics. This will be 0, unless you are
doing non-equilibrium dynamics. You can ignore or remove
this term, since you will not need it. <br>
<br>
Cheers, <br>
<br>
Berk <br>
<br>
On 2016-10-06 11:25, Elena della Valle wrote: <br>
<blockquote type="cite"> <br>
Okey but in the update.c file line 300, in the following
equation : v[n][d] = mv1*(mv1*v[n][d] +
0.5*(w_dt*mv2*f[n][d]))+0.5*accel[ga][d]*dt; <br>
with the term "0.5*accel[ga][d]*dt" it corresponds to the
term "[1/2*(∆t/m)* F(t + ∆t)] " in the verlet algorithm ?
<br>
Thanks in advance for helping me <br>
Best Regards <br>
Elena della Valle <br>
<br>
Il 06/10/2016 09:30, Berk Hess ha scritto: <br>
<blockquote type="cite">Hi, <br>
<br>
I guess you mean ga = cACC[n]. <br>
cACC[n] contains the acceleration group index for atom
n. This is for non-equilibrium dynamics where groups of
atom are accelerated. <br>
(apologies for the cryptic notation without
documentation) <br>
<br>
Cheers, <br>
<br>
Berk <br>
<br>
On 2016-10-06 07:44, Elena Della valle wrote: <br>
<blockquote type="cite">Hi, I have just a last question
what gromacs means exactly with the term: cACC[ga]? <br>
Thanks in advance <br>
Best Regards <br>
Elena della Valle <br>
<br>
<br>
<br>
<blockquote type="cite">Il giorno 04 ott 2016, alle
ore 17:58, Berk Hess <a moz-do-not-send="true"
class="moz-txt-link-rfc2396E"
href="mailto:hess@kth.se"><hess@kth.se></a>
ha scritto: <br>
<br>
<blockquote type="cite">On 10/04/2016 05:36 PM,
David van der Spoel wrote: <br>
<blockquote type="cite">On 04/10/16 17:00, Elena
Della valle wrote: <br>
I used the gromacs 4.6.5 <br>
Best regards <br>
Elena della Valle <br>
</blockquote>
Crudely put we do not support that version
anymore, so if you would like to have this
considered for inclusion in gromacs you would have
to implement it in the master branch and upload it
to gerrit. Whether it is correct you should test
your self using some known cases and carefully
constructed inputs. <br>
</blockquote>
In addition, even when you are not interested in
contributing the code, all developer work with the
most recent versions, so it's easier for us to help
you with the master version, especially for code
that has changed a lot over the past years like the
Velocity Verlet integrator. (And I think anyone
should prefer the latest version for development, so
one doesn't end up with functionality that only
works in 5 year old code.) <br>
<br>
Cheers, <br>
<br>
Berk <br>
<blockquote type="cite">Maybe you can also answer
the question when a magnetic effect would be
important? <br>
<blockquote type="cite"> <br>
<blockquote type="cite">
<blockquote type="cite">Il giorno 04 ott 2016,
alle ore 16:49, David van der Spoel <a
moz-do-not-send="true"
class="moz-txt-link-rfc2396E"
href="mailto:spoel@xray.bmc.uu.se"><spoel@xray.bmc.uu.se></a>
ha scritto: <br>
<br>
On 04/10/16 15:15, Elena della Valle wrote:
<br>
<br>
Hi to all, <br>
<br>
I'm Elena della Valle, a Ph.D. student
coming from la Sapienza <br>
University of Rome. <br>
<br>
I'm writing because I have some questions
about some modifications that <br>
I have done to the update of velocities and
positions in the verlet <br>
algorithm. My aim is to implement the
magnetic field in gromacs by <br>
introducing the therm of the larmor
frequency to the velocities and <br>
positions. By literature I read that this
has been done by the update of <br>
the verlet velocities and positions with the
frequency larmor therm. <br>
These are the equations in order to be more
clear on what i wanted to do: <br>
<br>
I did this by modifying in the update.c file
in gromacs the <br>
update_do_vv_vel and update_do_vv_pos ad
follows: <br>
<br>
if ((ptype[n] != eptVSite) &&
(ptype[n] != eptShell) &&
!nFreeze[gf][d]) <br>
{ <br>
v[n][0] = mv1*(mv1*v[n][0] +
<br>
0.5*(w_dt*mv2*f[n][0]))+0.5*accel[ga][0]*dt
+ <br>
w_dt*charge[n]*campoB*v[n][1]*mv1*mv1 + <br>
0.25*dt*invmass[n]*charge[n]*campoB*((w_dt*mv2*mv1*f[n][1]) + <br>
accel[ga][1]*dt
-2*w_dt*charge[n]*campoB*mv1*mv1*v[n][0]); <br>
v[n][1] = mv1*(mv1*v[n][1] +
<br>
0.5*(w_dt*mv2*f[n][1]))+0.5*accel[ga][1]*dt
+ <br>
w_dt*charge[n]*campoB*v[n][0]*mv1*mv1 - <br>
0.25*dt*invmass[n]*charge[n]*campoB*((w_dt*mv2*mv1*f[n][0]) + <br>
accel[ga][0]*dt
+2*w_dt*charge[n]*campoB*mv1*mv1*v[n][1]); <br>
v[n][2] = mv1*(mv1*v[n][2] +
<br>
0.5*(w_dt*mv2*f[n][2]))+0.5*accel[ga][2]*dt;
<br>
<br>
<br>
<br>
//printf("frame %lf \n", mv1); <br>
// printf("frame %d:
%lf\t%lf%lf\n", n, v[n][0], v[n][1], <br>
v[n][2]); <br>
} <br>
<br>
in the do_update_vv_pos: <br>
<br>
if ((ptype[n] != eptVSite) &&
(ptype[n] != eptShell) &&
!nFreeze[gf][d]) <br>
{ <br>
xprime[n][0] =
mr1*(mr1*x[n][0]+mr2*dt*v[n][0]) + <br>
mr1*0.5*dt*(w_dt*mr2*f[n][0] +
w_dt*charge[n]*campoB*v[n][1]*mr1); <br>
xprime[n][1] =
mr1*(mr1*x[n][1]+mr2*dt*v[n][1]) + <br>
mr1*0.5*dt*(w_dt*mr2*f[n][1] -
w_dt*charge[n]*campoB*v[n][0]*mr1); <br>
xprime[n][2] =
mr1*(mr1*x[n][2]+mr2*dt*v[n][2]) + <br>
mr1*0.5*dt*(w_dt*mr2*f[n][2]); <br>
} <br>
<br>
<br>
After that in the grompp file I modified the
integrator in md-vv and I <br>
run the simulation and it seems to use the
position and velocities <br>
modifications. <br>
<br>
I want know if you think that this way is
correct, if I implemented in <br>
the right way <br>
<br>
And Also I would like to know if in the
grompp file I have to modify <br>
other parameters (I use a beredensed
coupling) <br>
<br>
Thanks in advance <br>
Sorry for bothering you <br>
Best Regards <br>
Elena della Valle <br>
<br>
-- <br>
Elena della Valle <br>
Ph.D. Student in Electronic Engineering <br>
<br>
Department of Information Engineering,
Electronics and Telecommunications <br>
Sapienza, University of Rome <br>
via Eudossiana, 18 00184 Rome <br>
<br>
<br>
<br>
</blockquote>
Just a quick question: which version did you
use? All development should be in the master
version and this looks like uses something
older. <br>
<br>
<br>
<br>
-- <br>
David van der Spoel, Ph.D., Professor of
Biology <br>
Dept. of Cell & Molec. Biol., Uppsala
University. <br>
Box 596, 75124 Uppsala, Sweden. Phone:
+46184714205. <br>
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<pre class="moz-signature" cols="72">--
Elena della Valle
Ph.D. Student in Electronic Engineering
Department of Information Engineering, Electronics and Telecommunications
Sapienza, University of Rome
via Eudossiana, 18 00184 Rome</pre>
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<pre class="moz-signature" cols="72">--
Elena della Valle
Ph.D. Student in Electronic Engineering
Department of Information Engineering, Electronics and Telecommunications
Sapienza, University of Rome
via Eudossiana, 18 00184 Rome</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Elena della Valle
Ph.D. Student in Electronic Engineering
Department of Information Engineering, Electronics and Telecommunications
Sapienza, University of Rome
via Eudossiana, 18 00184 Rome</pre>
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