John Shultz wrote:
Why do I get this message saying the group is empty?
Analysing residue names:
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
There are: 11350 OTHER residues
There are: 244 PROTEIN residues
There are: 0 DNA residues
Analysing Protein...
Analysing Other...
0 System : 37770 atoms
1 Protein : 3848 atoms
2 Protein-H : 1980 atoms
3 C-alpha : 244 atoms
4 Backbone : 732 atoms
5 MainChain : 974 atoms
6 MainChain+Cb : 1206 atoms
7 MainChain+H : 1198 atoms
8 SideChain : 2650 atoms
9 SideChain-H : 1006 atoms
10 Prot-Masses : 3848 atoms
11 Non-Protein : 33922 atoms
12 LIG : 35 atoms
13 SOL : 33807 atoms
14 Na : 46 atoms
15 Cl : 34 atoms
16 Other : 33922 atoms
nr : group ! 'name' nr name 'splitch' nr Enter: list groups
'a': atom & 'del' nr 'splitres' nr 'l': list residues
't': atom type | 'keep' nr 'splitat' nr 'h': help
'r': residue 'res' nr 'chain' char
"name": group 'case': case sensitive 'q': save and quit
12 & 1
Copied index group 12 'LIG'
Copied index group 1 'Protein'
Merged two groups with AND: 35 3848 -> 0
Group is empty
1 & 12
Copied index group 1 'Protein'
Copied index group 12 'LIG'
Merged two groups with AND: 3848 35 -> 0
Group is empty
The use of & tells make_ndx to write out a group that is the intersection of
these two. If there are no overlaps, the group is empty. What you want is the
"or" operator:
12 | 1
-Justin
On Sat, May 22, 2010 at 9:57 AM, Justin A. Lemkul <jalem...@vt.edu> wrote:
John Shultz wrote:
Justin,
I finally got a chance to get back to this. I read the make_ndx
instructions. Unless I am mistaken, I guess that is what you use to
merge groups.
Yep, that's the purpose of make_ndx.
-Justin
Thanks,
Jack
On Thu, May 13, 2010 at 9:15 AM, Justin A. Lemkul <jalem...@vt.edu> wrote:
John Shultz wrote:
Thank you Justin, is there a way I can choose both Protein LIG? It has
the following options for me
You need to make a custom group that merges these two.
-Justin
Reading toplogy and shit from md.tpr
Reading file md.tpr, VERSION 4.0.5 (single precision)
50000 steps (100 ps) remaining from first run.
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
Group 0 ( System) has 37770 elements
Group 1 ( Protein) has 3848 elements
Group 2 ( Protein-H) has 1980 elements
Group 3 ( C-alpha) has 244 elements
Group 4 ( Backbone) has 732 elements
Group 5 ( MainChain) has 974 elements
Group 6 (MainChain+Cb) has 1206 elements
Group 7 ( MainChain+H) has 1198 elements
Group 8 ( SideChain) has 2650 elements
Group 9 ( SideChain-H) has 1006 elements
Group 10 ( Prot-Masses) has 3848 elements
Group 11 ( Non-Protein) has 33922 elements
Group 12 ( LIG) has 35 elements
Group 13 ( SOL) has 33807 elements
Group 14 ( Na) has 46 elements
Group 15 ( Cl) has 34 elements
Group 16 ( Other) has 33922 elements
Select a group:
On Thu, May 13, 2010 at 9:02 AM, Justin A. Lemkul <jalem...@vt.edu>
wrote:
John Shultz wrote:
I am trying to rerun a simulation using this command
mdrun -rerun -v -deffnm md
I think I must have made a mistake when I prepared the original mdp
file because I get this message
Number of atoms in trajectory (3883) does not match the run input file
(37770)
I have these files in my directory
Complex.top ener.edr job.xml md.cpt md.edr md.gro md.log md.mdp
md_prev.cpt md.tpr md.trr md.xtc traj.trr
Here is my mdp file, should I remove entries for xtc_grps and
energygrps to avoid this issue?
You can, but it won't fix anything. Your original .xtc file saved only
the
coordinates of the Protein and LIG (per your output options), but your
.tpr
file has all of these atoms, regardless of what you choose to save.
You
can, however, create a .tpr file that has a just these atoms by passing
your
original .tpr file to tpbconv, using a suitable index group.
-Justin
integrator = md
nsteps = 50000
dt = 0.002
nstvout = 5000
nstlog = 500
nstenergy = 250
nstxtcout = 5000
nstxout = 5000
xtc_grps = Protein LIG
energygrps = Protein SOL
constraints = all-bonds
nstcomm = 1
ns_type = grid
rlist = 1.2
rcoulomb = 1.1
rvdw = 1.0
vdwtype = shift
rvdw-switch = 0.9
coulombtype = PME-Switch
Tcoupl = v-rescale
tau_t = 0.1 0.1
tc-grps = protein non-protein
ref_t = 300 300
Pcoupl = parrinello-rahman
PcOupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
gen_vel = yes
lincs-iter = 2
DispCorr = EnerPres
optimize_fft = yes
gen_seed = 805087
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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or send it to gmx-users-requ...@gromacs.org.
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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