And what if I have four helices in Protein and a,b,c,d group for each helix in index.file and I want to get a-c pmf?<br><br><br><div class="gmail_quote">10 ฯหิัยาั 2010ว. 21:20 ะฯฬฺุฯืมิลฬุ Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> ฮมะษำมฬ:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><br>
<br>
Justin A. Lemkul wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
<br>
๐ลิา ๐ฯะฯื wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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 nsteps = 25000 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>
</blockquote></blockquote>
<br></div>
If this .mdp file is to be used for a rerun, please recall the advice I gave you earlier about the proper setting for nstlist.<br><font color="#888888">
<br>
-Justin</font><div><div></div><div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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>
</blockquote>
<br>
You cannot use multiple energygrps if those groups overlap in any way, as the error indicates. I thought you were setting "energygrps = Protein SOL"? If you're trying to get protein-only terms, then just set "energygrps = Protein"<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
<br>
10 ฯหิัยาั 2010 ว. 20:01 ะฯฬฺุฯืมิลฬุ ๐ลิา ๐ฯะฯื <<a href="mailto:magistrpetrus@gmail.com" target="_blank">magistrpetrus@gmail.com</a> <mailto:<a href="mailto:magistrpetrus@gmail.com" target="_blank">magistrpetrus@gmail.com</a>>> ฮมะษำมฬ:<br>
<br>
Thank you very much!<br>
<br>
10 ฯหิัยาั 2010 ว. 19:58 ะฯฬฺุฯืมิลฬุ Justin A. Lemkul<br>
<<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>>> ฮมะษำมฬ:<br>
<br>
<br>
<br>
๐ลิา ๐ฯะฯื wrote:<br>
<br>
So if I want to get protein-solvent component I should add<br>
in .mdp:<br>
<br>
energygrps = Protein SOL<br>
<br>
?<br>
<br>
<br>
Yes, and set nstlist = 1.<br>
<br>
-Justin<br>
<br>
10 ฯหิัยาั 2010 ว. 16:41 ะฯฬฺุฯืมิลฬุ Justin A. Lemkul<br>
<<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>><br>
<mailto:<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>>>> ฮมะษำมฬ:<br>
<br>
<br>
<br>
<br>
๐ลิา ๐ฯะฯื wrote:<br>
<br>
Thank you for response!<br>
One more question:<br>
How can I get file with energy groups? Should I use<br>
grompp with<br>
a -e ener.edr option? In this case, how to build<br>
ener.edr file?<br>
<br>
<br>
The "energrygrps" keyword is an .mdp option, so generate<br>
a new .tpr<br>
file with the desired groups and use the -rerun feature<br>
of mdrun on<br>
the trajectory that has already been produced.<br>
<br>
-Justin<br>
<br>
9 ฯหิัยาั 2010 ว. 14:50 ะฯฬฺุฯืมิลฬุ Mark Abraham<br>
<<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><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><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><br>
<mailto:<a href="mailto:mark.abraham@anu.edu.au" target="_blank">mark.abraham@anu.edu.au</a>>>>> ฮมะษำมฬ:<br>
<br>
<br>
You can get that with cunning use of energy groups<br>
and mdrun<br>
-rerun,<br>
but not mid-simulation.<br>
Mark<br>
<br>
----- Original Message -----<br>
From: ๐ลิา ๐ฯะฯื <<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>
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<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>
<mailto:<a href="mailto:magistrpetrus@gmail.com" target="_blank">magistrpetrus@gmail.com</a>><br>
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<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><br>
<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>
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<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<br>
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<br>
protein-solvent<br>
interactions or protein-protein interactions or<br>
solvent-solvent<br>
interactions instead and get output .xvg file in<br>
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<br>
help me!<br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
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-- ========================================<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>
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Department of Biochemistry<br>
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Blacksburg, VA<br>
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========================================<br>
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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>
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