Yes, I did one md step and got all non-zero forces.<br>But for the energy minimization, all the forces are zero, althouth mdrun command gives non-zero forces.<br><br><div class="gmail_quote">On Sun, Jun 28, 2009 at 4:23 AM, Florian Dommert <span dir="ltr"><<a href="mailto:dommert@icp.uni-stuttgart.de">dommert@icp.uni-stuttgart.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">* Shuangxing Dai <<a href="mailto:shuangxingdai@gmail.com" target="_blank">shuangxingdai@gmail.com</a>> [2009-06-27 20:22:13 -0600]:<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Yes, they are all zeros. I am confused why this happen. Thank you for help.<br>
And here is the mdp file:<br>
</blockquote>
<br></div>
That would confuse me, too. As I have never analyzed forces from a<br>
energy minimization, perhaps there is the problem. Try a zero-step md,<br>
meaning integrator=md and nsteps=0 and leave the further parameters<br>
unchanged. In case you get forces in your analysis then, we have<br>
discovered the source of error :)<br>
<br>
/Flo<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5">
; RUN CONTROL PARAMETERS =<br>
integrator = steep<br>
nsteps = 50<br>
; Output frequency for coords (x), velocities (v) and forces (f)<br>
nstxout = 1<br>
nstvout = 1<br>
nstfout = 1<br>
; Output frequency for energies to log file and energy file<br>
nstlog = 1<br>
nstenergy = 1<br>
; Output frequency and precision for xtc file<br>
nstxtcout = 1<br>
xtc-precision = 1000<br>
; ENERGY MINIMIZATION OPTIONS =<br>
; Force tolerance and initial step-size =<br>
emtol = 1<br>
emstep = 0.01<br>
; NEIGHBORSEARCHING PARAMETERS =<br>
; nblist update frequency =<br>
nstlist =3<br>
; ns algorithm (simple or grid) =<br>
ns_type = simple<br>
; Periodic boundary conditions: xyz or none =<br>
pbc = xyz<br>
; nblist cut-off =<br>
rlist =0.9<br>
; OPTIONS FOR ELECTROSTATICS AND VDW =<br>
; Method for doing electrostatics =<br>
coulombtype = Shift<br>
rcoulomb = 0.9<br>
; Dielectric constant (DC) for cut-off or DC of reaction field =<br>
epsilon-r = 1<br>
; Method for doing Van der Waals =<br>
vdw-type = Cut-off<br>
; cut-off lengths =<br>
rvdw = 0.9<br>
; Spacing for the PME/PPPM FFT grid =<br>
fourierspacing = 0.1<br>
; FFT grid size, when a value is 0 fourierspacing will be used =<br>
fourier_nx = 0<br>
fourier_ny = 0<br>
fourier_nz = 0<br>
; EWALD/PME/PPPM parameters =<br>
pme_order = 6<br>
ewald_rtol = 1e-05<br>
epsilon_surface = 0<br>
optimize_fft = no<br>
<br>
And also another question, can Gromacs write out the energy for each atom at<br>
each step? Just like it did to the forces? I use this mdp file and only see<br>
the total energy for each step in the log file.<br>
Thanks again.<br>
<br>
On Sat, Jun 27, 2009 at 8:07 PM, Florian Dommert <<br>
<a href="mailto:dommert@icp.uni-stuttgart.de" target="_blank">dommert@icp.uni-stuttgart.de</a>> wrote:<br>
<br>
</div></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5">
* Shuangxing Dai <<a href="mailto:shuangxingdai@gmail.com" target="_blank">shuangxingdai@gmail.com</a>> [2009-06-27 18:57:41 -0600]:<br>
<br>
The nstfout =1 in mdout.mdp. So this should not be where the problem is.<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
</blockquote>
<br>
So this was the most obvious mistake I could imagine and you see it is<br>
always appreciated that you put your mdp file also to the list, that<br>
everybody knows your input parameters. However in case you already told<br>
gromacs to write out the data to the trr file it should be there.<br>
So if you try:<br>
<br>
echo 0 | g_traj -f traj.trr -s topol.tpr -of<br>
Only zeros are contained in force.xvg ??<br>
<br>
/Flo<br>
<br>
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
----- Original Message ----- From: "Florian Dommert" <<br>
<a href="mailto:dommert@icp.uni-stuttgart.de" target="_blank">dommert@icp.uni-stuttgart.de</a>><br>
To: "Discussion list for GROMACS users" <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Sent: Saturday, June 27, 2009 3:20 PM<br>
Subject: Re: [gmx-users] force<br>
<br>
<br>
_______________________________________________<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>
posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
</blockquote>
<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>
posting!<br>
Please don't post (un)subscribe requests to the list. Use the www<br>
interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
</blockquote>
<br>
--<br>
Florian Dommert<br>
Dipl.-Phys.<br>
<br>
Institute for Computational Physics<br>
University Stuttgart<br>
<br>
Pfaffenwaldring 27<br>
70569 Stuttgart<br>
<br>
Tel: +49 - 711 / 6856-3613<br>
Fax: +49 - 711 / 6856-3658<br>
<br>
EMail: <a href="mailto:dommert@icp.uni-stuttgart.de" target="_blank">dommert@icp.uni-stuttgart.de</a><br></div></div>
Home: <a href="http://www.icp.uni-stuttgart.de/%7Eicp/Florian_Dommert" target="_blank">http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert</a><<a href="http://www.icp.uni-stuttgart.de/%7Eicp/Florian_Dommert" target="_blank">http://www.icp.uni-stuttgart.de/%7Eicp/Florian_Dommert</a>><div class="im">
<br>
<br>
!! PGP-ENCODED emails preferred !!<br>
<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
</div></blockquote>
<br>
<br>
<br>
-- <br>
Shuangxing Dai<br>
</blockquote><div><div></div><div class="h5">
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</blockquote>
<br>
-- <br>
Florian Dommert<br>
Dipl.-Phys.<br>
<br>
Institute for Computational Physics<br>
University Stuttgart<br>
<br>
Pfaffenwaldring 27<br>
70569 Stuttgart<br>
<br>
Tel: +49 - 711 / 6856-3613<br>
Fax: +49 - 711 / 6856-3658<br>
<br>
EMail: <a href="mailto:dommert@icp.uni-stuttgart.de" target="_blank">dommert@icp.uni-stuttgart.de</a><br>
Home: <a href="http://www.icp.uni-stuttgart.de/%7Eicp/Florian_Dommert" target="_blank">http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert</a><br>
<br>
!! PGP-ENCODED emails preferred !!<br>
</div></div><br>_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br><br clear="all"><br>-- <br>Shuangxing Dai<br>