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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>
<blockquote 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:part1.D48C5124.28817FB8@kth.se" 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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