I already knew the reason. But I had to find this out hard way. Now facing a dreading prospect of repeating tons of calculations! Hence the request for the "bad for the health" sign. Btw, gromacs issues a lot of warnings, but not this one :D<div>
<div><br></div><div>What a bright idea to switch from angstroms to nanometers! Now the gro files carry a lot of useless zeros.</div><div><br></div><div> On Sat, Nov 26, 2011 at 3:55 PM, <span dir="ltr"><<a href="mailto:chris.neale@utoronto.ca" target="_blank">chris.neale@utoronto.ca</a>></span> wrote:<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
There is rounding because of angstroms vs nanometers and both files maintain 3 decimal places (see below).<br>
<br>
The intention of pdb2gmx is not to get a .gro , but to get a .top or .itp file.<br>
<br>
I see your point, but I don't think it matters. If you really need that precision, then I'd think that you'd be using double precision gromacs (which would still round the output .gro from pdb2gmx and not solve this issue... just saying).<br>
<br>
gpc-f101n084-$ tail a.gro<br>
2GLY HA2 11 -0.426 0.215 0.193<br>
2GLY C 12 -0.446 0.390 0.072<br>
2GLY O 13 -0.368 0.440 -0.013<br>
3NME N 14 -0.532 0.478 0.154<br>
3NME H 15 -0.618 0.488 0.104<br>
3NME CH3 16 -0.468 0.607 0.173<br>
3NME HH31 17 -0.375 0.594 0.227<br>
3NME HH32 18 -0.533 0.670 0.234<br>
3NME HH33 19 -0.447 0.661 0.081<br>
0.47330 0.80470 0.29640<br>
gpc-f101n084-$ tail a.pdb<br>
ATOM 11 HA2 GLY 2 -4.263 2.147 1.932<br>
ATOM 12 C GLY 2 -4.461 3.901 0.720<br>
ATOM 13 O GLY 2 -3.677 4.400 -0.128<br>
HETATM 14 N NME 3 -5.316 4.776 1.535<br>
HETATM 15 H NME 3 -6.182 4.876 1.044<br>
HETATM 16 CH3 NME 3 -4.685 6.072 1.731<br>
HETATM 17 1HH3 NME 3 -3.754 5.941 2.272<br>
HETATM 18 2HH3 NME 3 -5.328 6.697 2.341<br>
HETATM 19 3HH3 NME 3 -4.465 6.615 0.809<br>
END<br>
<br>
-- original message --<br>
<br>
There was no water. Version 4.5.5. Single precision. This is what I ran:<br>
<br>
pdb2gmx -f 1.pdb -p g1 -o g1<br>
grompp -f 1.mdp -c g1.gro -o g1.tpr -p g1.top<br>
mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene<br>
Potential energy: 1.19780e+02 kJ/mol<br>
<br>
grompp -f 1.mdp -c 1.pdb -o g1.tpr -p g1.top<br>
mdrun -v -s g1.tpr -c ag1.gro -g g1.log -e g1.ene<br>
Potential energy: 1.15997e+02 kJ/mol<br>
<br>
The mdp file:<br>
<br>
integrator = md<br>
nsteps = 0<br>
nstcomm = 1<br>
nstxout = 1<br>
nstvout = 1<br>
nstfout = 0<br>
nstlog = 1<br>
nstenergy = 1<br>
nstxtcout = 0<br>
nstlist = 0<br>
ns_type = simple<br>
pbc = no<br>
rlist = 0<br>
rcoulomb = 0<br>
rvdw = 0<br>
gen_vel = no<br>
unconstrained-start = yes<br>
lincs-warnangle = 30<br>
<br>
The pdb file :<br>
<br>
HETATM 1 1HH3 ACE 1 -1.449 0.109 -0.581<br>
H<br>
HETATM 2 CH3 ACE 1 -2.101 -0.268 0.202<br>
C<br>
HETATM 3 2HH3 ACE 1 -1.708 0.090 1.151<br>
H<br>
HETATM 4 3HH3 ACE 1 -2.109 -1.350 0.189<br>
H<br>
HETATM 5 C ACE 1 -3.491 0.269 0.000<br>
C<br>
HETATM 6 O ACE 1 -4.453 -0.401 -0.152<br>
O<br>
ATOM 7 N GLY 2 -3.601 1.734 0.000<br>
N<br>
ATOM 8 H GLY 2 -3.039 2.278 -0.623<br>
H<br>
ATOM 9 CA GLY 2 -4.525 2.391 0.903<br>
C<br>
ATOM 10 HA1 GLY 2 -5.539 2.051 0.696<br>
H<br>
ATOM 11 HA2 GLY 2 -4.263 2.147 1.932<br>
H<br>
ATOM 12 C GLY 2 -4.461 3.901 0.720<br>
C<br>
ATOM 13 O GLY 2 -3.677 4.400 -0.128<br>
O<br>
HETATM 14 N NME 3 -5.316 4.776 1.535<br>
N<br>
HETATM 15 H NME 3 -6.182 4.876 1.044<br>
H<br>
HETATM 16 CH3 NME 3 -4.685 6.072 1.731<br>
C<br>
HETATM 17 1HH3 NME 3 -3.754 5.941 2.272<br>
H<br>
HETATM 18 2HH3 NME 3 -5.328 6.697 2.341<br>
H<br>
HETATM 19 3HH3 NME 3 -4.465 6.615 0.809<br>
H<br>
END<br>
<br>
<br>
*In reply to chris.neale at utoronto.ca:*<br>
<br>
It's more useful if you provide more information. What was the .pdb<br>
<br>
file (can I download it from the pdb databank?) was there water? what<br>
<br>
version of gromacs? was it compiled in double or single precision?<br>
<br>
what were your mdp parameters?<span><font color="#888888"><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/<u></u>mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use thewww 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/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists</a><br>
</font></span></blockquote></div><br>
</div></div>