Hello dear gmx-users!<br><br>So, I run md and got all files md.cpt, .trr, .gro, mdf.xvg,... etc.<br>then I did: grompp_d -f sp.mdp -c md.gro -n index.ndx -p topol.top -o sp.tpr<br>where sp.mdp differ from md.mdp in one line: energygrps = Protein SOL (in md.mdp: energygrps = System)<br>
after that I did: mdrun_d -s sp.tpr -pf spf -rerun md.trr<br>and got file spf.xvg, but there was no forces:<br><br>@ title "Pull force"<br>@ xaxis label "Time (ps)"<br>@ yaxis label "Force (kJ/mol/nm)"<br>
@TYPE xy<br>0.000000 0.000000<br>20.000000 0.000000<br>40.000000 0.000000<br>60.000000 0.000000<br>80.000000 0.000000<br>100.000000 0.000000<br>
120.000000 0.000000<br>140.000000 0.000000<br>160.000000 0.000000<br>180.000000 0.000000<br>200.000000 0.000000<br><br>Also while reading frame I had a warning:<br>
<br> WARNING: Some frames do not contain velocities.<br> Ekin, temperature and pressure are incorrect,<br> the virial will be incorrect when constraints are present.<br><br>But I have no idea how to fix this.<br>
<br>Help me, please.<br><br>Sincerely.<br>Petr.<br><br><br><br><div class="gmail_quote">11 октября 2010 г. 6:33 пользователь Dallas Warren <span dir="ltr"><<a href="mailto:Dallas.Warren@monash.edu">Dallas.Warren@monash.edu</a>></span> написал:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div link="blue" vlink="purple" lang="EN-US">
<div>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">The error has told you, you have repeat energy groups, where at
least one (and in your case all) of the atoms are placed within two energy
groups.</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);">Solution, define your energy groups so that you don’t have
atoms in more than one.</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal">You currently have:</p>
<p class="MsoNormal">energygrps
= Protein Protein</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Should be something like</p>
<p class="MsoNormal">energygrps
= Protein SOL<span style="font-size: 11pt; color: rgb(31, 73, 125);"></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 10pt; color: rgb(31, 73, 125);">Catch ya,<br>
<br>
Dr. Dallas Warren</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; color: rgb(31, 73, 125);">Medicinal Chemistry and Drug Action</span></p>
<p class="MsoNormal"><span style="font-size: 10pt; color: rgb(31, 73, 125);">Monash Institute of Pharmaceutical Sciences</span><span style="font-size: 10pt; color: rgb(31, 73, 125);">,
Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<a href="mailto:dallas.warren@monash.edu" target="_blank">dallas.warren@monash.edu</a></span></p>
<p class="MsoNormal"><span style="font-size: 10pt; color: rgb(31, 73, 125);">+61 3 9903 9304<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a
nail.</span><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; color: rgb(31, 73, 125);"> </span></p>
<div style="border-width: medium medium medium 1.5pt; border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; padding: 0cm 0cm 0cm 4pt;">
<div>
<div style="border-width: 1pt medium medium; border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; padding: 3pt 0cm 0cm;">
<p class="MsoNormal"><b><span style="font-size: 10pt;">From:</span></b><span style="font-size: 10pt;">
<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>] <b>On
Behalf Of </b>???? ?????<br>
<b>Sent:</b> Monday, 11 October 2010 4:13 AM<br>
<b>To:</b> <a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>; Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] output force</span></p>
</div>
</div><div><div></div><div class="h5">
<p class="MsoNormal"> </p>
<p class="MsoNormal" style="margin-bottom: 12pt;">Unfortunately I've got an
error.<br>
<br>
This is .mdp file:<br>
<br>
title = title<br>
cpp
= /lib/cpp<br>
integrator = md<br>
tinit
= 0.0<br>
dt
= 0.002 <br>
nsteps
= 25000 <br>
nstcomm
= 1<br>
comm_grps =
System<br>
ld_seed
= -1<br>
niter
= 40<br>
nstxout
= 10000<br>
nstvout
= 0<br>
nstfout
= 0<br>
nstlog
= 500<br>
nstenergy =
100<br>
nstlist
= 10<br>
ns_type
= grid<br>
rlist
= 1.2<br>
coulombtype = PME<br>
rcoulomb
= 1.2<br>
fourierspacing = 0.12<br>
pme_order = 4<br>
optimize_fft = yes<br>
pbc
= xyz<br>
vdwtype
= Cut-off<br>
rvdw
= 1.2<br>
tcoupl
= V-rescale<br>
tc_grps
= System<br>
tau_t
= 0.1<br>
ref_t
= 300.0<br>
annealing = single<br>
annealing_npoints = 3<br>
annealing_time = 0 5 50<br>
annealing_temp = 5 300 300<br>
pcoupl
= berendsen<br>
pcoupltype =
isotropic<br>
compressibility = 4.5e-5<br>
tau_p
= 10.0<br>
ref_p
= 1.0<br>
gen_vel
= yes<br>
gen_temp
= 5.0<br>
gen_seed
= -1<br>
constraints = all-bonds<br>
constraint_algorithm = Lincs<br>
lincs_order = 4<br>
disre
= simple<br>
disre_weighting = conservative<br>
disre_mixed = no<br>
nstdisreout = 50000<br>
disre_tau = 0<br>
pull
= constraint<br>
pull_geometry = distance<br>
pull_dim = Y
Y Y<br>
pull_constr_tol = 1e-6<br>
pull_nstfout = 1<br>
pull_nstxout = 1<br>
pull_ngroups = 1<br>
pull_group0 = a<br>
pull_group1 = b<br>
pull_init1 = 0.700<br>
pull_start = no<br>
pull_k1
= 1000<br>
lincs_iter = 2<br>
energygrps = Protein
Protein<br>
<br>
I just replace in .mdp file line energygrps = System and the error is:<br>
<br>
Fatal error:<br>
Atom 1 in multiple Energy Mon. groups (1 and 2)<br>
<br>
What should I do to avoid this?<br>
<br>
<br>
</p>
<div>
<p class="MsoNormal">10 октября 2010 г. 20:01 пользователь Петр Попов <<a href="mailto:magistrpetrus@gmail.com" target="_blank">magistrpetrus@gmail.com</a>> написал:</p>
<p class="MsoNormal" style="margin-bottom: 12pt;">Thank you very much!</p>
<div>
<p class="MsoNormal">10 октября 2010 г. 19:58 пользователь Justin A. Lemkul
<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>
написал:</p>
<div>
<div>
<blockquote style="border-width: medium medium medium 1pt; border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color rgb(204, 204, 204); padding: 0cm 0cm 0cm 6pt; margin-left: 4.8pt; margin-right: 0cm;">
<p class="MsoNormal"> </p>
<div>
<p class="MsoNormal"><br>
<br>
Петр Попов wrote:</p>
<p class="MsoNormal" style="margin-bottom: 12pt;">So if I want to get
protein-solvent component I should add in .mdp:<br>
<br>
energygrps = Protein SOL<br>
<br>
?</p>
<p class="MsoNormal"> </p>
</div>
<p class="MsoNormal" style="margin-bottom: 12pt;">Yes, and set nstlist = 1.<br>
<br>
-Justin</p>
<p class="MsoNormal">10 октября 2010 г. 16:41 пользователь Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>
написал:</p>
<div>
<p class="MsoNormal"><br>
<br>
<br>
<br>
Петр Попов wrote:<br>
<br>
Thank you for response!<br>
One more question:<br>
How can I get file with energy groups? Should I use
grompp with<br>
a -e ener.edr option? In this case, how to build
ener.edr file?<br>
<br>
<br>
The "energrygrps" keyword is an .mdp option, so generate
a new .tpr<br>
file with the desired groups and use the -rerun feature of mdrun
on<br>
the trajectory that has already been produced.<br>
<br>
-Justin<br>
<br>
9 октября 2010 г. 14:50 пользователь Mark Abraham<br>
<<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a> <mailto:<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a>><br>
<mailto:<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a><br>
<mailto:<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a>>>> написал:<br>
<br>
<br>
You can get that with cunning use of energy
groups and mdrun<br>
-rerun,<br>
but not mid-simulation.<br>
Mark<br>
<br>
----- Original Message -----<br>
From: Петр Попов <<a href="mailto:magistrpetrus@gmail.com" target="_blank">magistrpetrus@gmail.com</a><br>
<mailto:<a href="mailto:magistrpetrus@gmail.com" target="_blank">magistrpetrus@gmail.com</a>></p>
</div>
<div>
<p class="MsoNormal"> <mailto:<a href="mailto:magistrpetrus@gmail.com" target="_blank">magistrpetrus@gmail.com</a><br>
<mailto:<a href="mailto:magistrpetrus@gmail.com" target="_blank">magistrpetrus@gmail.com</a>>>><br>
Date: Saturday, October 9, 2010 21:41<br>
Subject: [gmx-users] output force<br>
To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>></p>
</div>
<div>
<div>
<p class="MsoNormal"> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>><br>
<br>
> Hello dear gmx-users!<br>
><br>
> When calculated forces in gromacs
to produce pmf, we have<br>
the net<br>
force in output. For example:<br>
> ...<br>
> #<br>
> # Giving Russians Opium May Alter
Current Situation<br>
> #<br>
> @ title "Pull
force"<br>
> @ xaxis label
"Time (ps)"<br>
> @ yaxis label
"Force (kJ/mol/nm)"<br>
> @TYPE xy<br>
> 0.000000
1017490.761270<br>
> 0.002000
-253098.034916<br>
> 0.004000
-43856.400160<br>
> 0.006000
48980.619113<br>
> 0.008000
52103.053067<br>
> 0.010000
33788.090031<br>
> 0.012000
19096.388350<br>
> 0.014000
14094.738810<br>
> 0.016000
14027.621966<br>
> 0.018000
15162.993741<br>
> 0.020000
14136.978177<br>
> ... etc.<br>
><br>
> What sould I do to get the net
force of protein-solvent<br>
interactions or protein-protein interactions
or solvent-solvent<br>
interactions instead and get output .xvg
file in the form<br>
like this:<br>
><br>
> time Force(type1)
Force(type2) Force(type3)<br>
><br>
> t1 f1
f1
f1<br>
> t2 f2
f2
f2<br>
> t3 f3
f3
f3<br>
> ...
... ...
...<br>
> etc.<br>
><br>
> Thank you for attention and I
hope you will help me!<br>
> --<br>
> gmx-users mailing list
<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>></p>
</div>
</div>
<p class="MsoNormal"> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>></p>
<div>
<p class="MsoNormal"><br>
<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<br>
> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/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>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>>.<br>
<br>
> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>></p>
</div>
<p class="MsoNormal"> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>></p>
<div>
<p class="MsoNormal"><br>
<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<br>
<a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/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>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a></p>
</div>
<div>
<p class="MsoNormal"> <mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>>.<br>
<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
<br>
<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA</p>
</div>
<p class="MsoNormal"> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>>
| (540) 231-9080</p>
<div>
<p class="MsoNormal" style="margin-bottom: 12pt;"><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
-- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<mailto:<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<br>
<a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before
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>
<mailto:<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/Support/Mailing_Lists</a><br>
<br>
</p>
</div>
<div>
<div>
<p class="MsoNormal"><br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<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/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a></p>
</div>
</div>
</blockquote>
</div>
</div>
</div>
<p class="MsoNormal"> </p>
</div>
<p class="MsoNormal"> </p>
</div></div></div>
</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/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br>