Dear all
I want to know what is difference between -ee option in the g_analyze which
gives error estimate using block averaging and usual standard deviation or
variance?
which of them have advantage?
Any help will highly appreciated.
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Dear gromacs user
I did simulation of carbon nanotube (one in center and 6 in the
vicinity of that)|:
every CNT have 120 atoms.
1) energy minimization
2) equilibration in NVT ensemble
when I did equilibration in NPT ensemble, I encountered Fatal error:
Number of grid cells is zero. Probably
Dear Justin
I'm using your script for obtaining %exist of hydrogen bonds.
When I use ./hb.pl structure.pdb -map hbmap.xpm -index hbond.ndx, I
encountered with
No -map specified!
I noted to points being at the begining of script:
# 1. coordinate file (for atom naming) - MUST be a .pdb file
Dear Tsjerk and Mark
Thanks for your time and attention.
using g_select -f *.xtc -s *.tpr -n index.ndx -oi -select 'Close to
Protein resname SOL and within 0.25 of group Protein' solved my problem.
I want to use trjorder -f *.xtc -s *.tpr -n index.ndx -o ordered.pdb
-nshell -r 0.25 -na 3 -da 1
Dear all
Which one of g_select and trjorder is the best for obtaining those water
molecules being within x nm of protein?
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Dear Justin
Thanks for your reply.
I know, with g_select, I obtain index groups that tell me which atoms
satisfy the given criteria and with trjorder, the coordinates of those
atoms are reordered such that they are listed in sequence in the new
trajectory. But g_select gives an output file
Dear Justin
You are wright. The two output files should not be equivalent.
If I want to know residue number of water molecules being within x nm of
protein, which tool is the best for me?
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Dear Justin
If I want to know residue number of water molecules being within x nm of
protein, for each frame, which tool is the best for me?
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Dear gromacs users
My system contains protein and water molecules.
I want to use g_select to obtain residue number of water molecules being
within 0.35 nm of protein.
My index file is as follows:
[ Protein ]
[SOL]
When I use g_select -f *.xtc -s *.tpr -n index.ndx -oi -select Close to
Dear Justin
Thanks for your reply.
As you said You need to enclose your selection string within ' ' so it is
interpreted as a single string. , I enclosed my selection string:
g_select -f com_ta_full_3.xtc -s com_ta_full.tpr -n index.ndx -oi -select
Close to Protein 'resname' 'SOL' and within
Dear gromacs users
I have a pdb file (10 base pair) containing a specific damage being my
favourite for md simulation study.
The damaged nucleic acid is in the last but one. I want to add at least 5
base pair to original pdb file.
How to do that? What program can help me?
Any help will
Dear all
I used g_analyze -f dist.xvg -ee
In the one of the my output files, I encountered
Read 1 sets of 1252 points, dt = 0.0119951
std. dev.relative deviation of
standard - cumulants from those of
set
Dear gromacs users
I want to calculate error estimates using block averaging for output from
g-dist
(distance between donor atom of protein and acceptor atom of dna).
I used g_analyze -f dist.xvg -ee
there are 3 columns in output file.
anyone give me more explain about these columns?
how to
Dear Mark
I am studying interaction between protein and dna, especially hydrogen
bonds. using g-dist, I obtained distance between donor atom of protein and
acceptor atom of dna.
in this case, can I use g_analyze for obtaining error bar or stddev?
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Dear Mark
can I obtain error bar twice the standard error of the average
distance between the donor atom of protein and acceptor atom of dna over 1
simulation?
should I do several simulation. Is 1 simulation enough?
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Dear all
For what parameters I can use g_analyze -av average.xvg -errbar stddev -f *.xvg?
Can I use above tool for obtaining error bars for a *.xvg file resulting
from g_dist?
I want to obtain a file (containing error bar) to plot with excel.
Best Regard
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Dear Mark
thanks for your reply.
I have a general questions:
For what parameters I can use g_analyze -av average.xvg -errbar stddev
-f *.xvg?*
What quantity do you wish to show with an error bar?
I want to show output from g_dist with an error bar.
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Dear gromacs users
I would like to calculate the standard deviation (as the error bar) for
rmsd.xvg file.
If rmsd.xvg was used in excel software, it gives a graph as rmsd vs time. I
want to have a file containing rmsd vs time
and error bar relating to rmsd values such that after plotting by
Dear gromacs users
In the average file, there are 3 columns:
first column is time, second is rmsd value.
third column is 0.
what is third column?
best regards.
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Dear Mark
Thanks for your quick reply.
For what parameters I can use g_analyze -av average.xvg -errbar stddev -f
*.xvg?
Can I use above tool for obtaining error bars for a *.xvg file resulting
from g_dist?
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Hi,
You should use trjconv in 2 steps:
(1) trjconv_d -s md_100ns.tpr -f md_100ns.xtc -o
md_100ns_pbc_nojump.xtc -pbc nojump
in this step, select system for output
(2) trjconv_d -s md_100ns.tpr -f md_100ns_pbc_nojump.xtc -o
md_100ns_pbc_mol_center.xtc -pbc mol -center
in this step, select
Dear gromacs users
I want to do MD simulation of protein-ligand.
I read a tutorial by John E. Kerrigan Tutorial for Trypsin-Benzamidine
complex molecular dynamics study. in which
they used acpype.
I want to know what is acpype? a program in gromacs or amber or a pythone
file? please explain
Dear Kavya
Thanks for your attention
Unfortunately, I don't access to http://code.google.com/p/acpype/
Your client does not have permission to get URL /p/acpype/ from this server.
Please guide me.
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Hi Nicole
In linux/unix, there are a program named xmgr aor xmgrace by default.
Just you type in command line : xmgr 1.xvg 2.xvg 3.xvg ..
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Dear Justin
Thanks for your attention
My problem was solved.
I have a new question. as I said my goal is superposition of averaged md
structure and x-ray structure.
My simulation is 5 ns. How to obtain the MD structure average for the period
1.5–5 ns? what command?
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Dear gromacs users
I want to know how to cite gromacs version 4.0.7? what paper do relate to
that?
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0.080
please explain this differences more.
best regards.
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, please guide me about that.
any suggestion will highly appreciated.
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ASN51 ND2 0.320
GLN23 OE111.191
.
.
.
how to fix it?
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Dear Justin
yes, I deleted my previous summary_HBmap.dat before running the
modified script.
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11.191
SOL1805OW LEU26 O0.160
SOL1805OW SER27 N0.160
best regards
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ARG58 NH1 0.080
ARG58 NH1 21.663
What is problem?
Please guide me about that.
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) {
copy_rvec(fr.f[index[i]],frout.f[i]);
}
}
}
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for example ordering in final.pdb is as follows:
ATOM 1856 N2 DG3 X 86 15.620 47.770 21.660 1.00
0.00
ATOM 1857 H21 DG3 X 86 16.480 48.290 21.560 1.00
0.00
ATOM 1858 H22 DG3 X 86 15.010 48.060 22.420 1.00
0.00
ATOM 1859 N3 DG3 X 86 14.160 46.250
,a,b,c=range,1867,24085,24099 wrong?
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Dear Chris
very thanks for your time and attention.
only difference between what you said and what I did is in the
location of template directory:
for me gromacs-4.0.7/share/template
for you gromacs-4.0.7/exec/share/gromacs/template
in my gromacs there is not exec directory even in fresh and
Dear Chris
Happy new year
thanks for your reply.
please clarify these more:
cd src/tools
cp gmx_trjconv.c ../../exec/share/gromacs/template/my_tool.c
1) where is exact location of gmx_trjconv.c file?
when I enter cd /src, in src directory, there is not tools directory.
2) in my linux,
Dear Chris
I found gmx_trjconv.c file, It is in gromacs-4.0.7/src/tools.
since location of template directory is as follows:
gromacs-4.0.7/share/template,
I used cp gmx_trjconv.c ../../share/template/my_tool.c.
is it true?
I did those changes you said in my_tool.c file.
I created makefile without
and suggestion will highly appreciated.
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Dear gromacs users
I used g_hbond tool for hydrogen bond analysis between protein and solvent
(water molecules).
I have encountered with :
Select a group: 3
Selected 3: 'Protein'
Select a group: 15
Selected 15: 'SOL'
Checking for overlap in atoms between Protein and SOL
Calculating hydrogen
Dear Erik
I used g_hbond in 4.5.1 but problem was not solved.
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a bugzilla and attach a tpr and xtc/trr? I don't know.
size of xtc file is large, how to attach this file to list?
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Dear Erik
excuse me, I sent .xtc and .tpr file your e-mail.
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Dear Erik
there are several hb-per-pHist in gmx_hbond.c.
please say me exactly in which part of the gmx_hbond.c file if-statement
should be placed?
If I install gromacs 4.5.2 or 4.5.3, is there not this problem (segmentation
fault)?
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K.N
Dear Oliver Grant
thanks for your attention.
I want to use amber tool for hydrogen bond analysis especially (water
mediated hydrogen bonds and residence time and occupation of them).
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to change the pdb file for compatibility
with amber.
please share me that.
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Dear gromacs users
I did simulation of protein-dna by gromacs and amber03 force field. I want
to do some analysis by amber. what is the best way for conversion of gromacs
trajectory and topology files to amber files?
any help will highly appreciated.
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? Is there problem in my .ndx file?
Is this error a bug in gromacs 4.5.1?
Leila Karami
Ph.D. student of Physical Chemistry
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Theoretical Physical Chemistry Group
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Please
protein and DNA* *and not protein or dna.*
*
*
*
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Dear Justin
I made new .ndx file in which there are following groups:
protein
protein-H
DNA
DNA-H
SOL
I changed selection.dat file to
waterO = group SOL and name OW;
heavy1 = group Protein-H;
heavy2 = group DNA-H;
inter = waterO and within 0.3 of heavy1 and within 0.3 of heavy2;
inter;
but
: trajana.c, line: 1310
Input error or input inconsistency:
selection(s) could not be parsed
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
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.
and also you said I need to create a corresponding index file too.
I don't know where should I start for multiply two existence functions?
please explain about it more.
any help will highly appreciated.
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the existence functions
how to multiply these two existence functions?
how to make new index file? should I write those lines from two hbond.ndx
file above in which particular water hbonds to both protein and DNA?
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.
3) I think that %exist should be determined for each of
donor-hydrogen-acceptor being in hbond.ndx file.Isn't it?
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, for obtaining of hbond.ndx
and hbmap.xpm files from g_hbond tool, what groups should be select?
in previous state (protein-dna direct hydrogen bond), I selected 1) protein
and 2) dna.
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Dear Erik
I'm confused. is there h(t) in hbmap.xpm file?
where is h(t)? which output file of g_hbond tool?
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Dear Justin
I study simulation of pr-dna complex. I want to know the percentage of
existence of each hbond during my trajectory.
I searched in previous lists. I want to use Perl script you offered to carla
jamous:
http://lists.gromacs.org/pipermail/gmx-users/2010-October/054727.html
I'm biginner
Dear Carla
thanks for your attention
I used : perl HB.pl -s .pdb -map .xpm -index .ndx, but problem is there yet.
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Dear Justin
thanks for your time and attention
yes of cource, I copy and paste correctly entire script from (first line) #
! /usr/bin/perl to (last line) exit. what is your mean of [There should be
more information in the output if the program fails]? which output?
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Dear Justin
when I use perl HB.pl -s .pdb -map .xpm -index .ndx, I encountered with:
syntax error at ./HB.pl line 10, near nothing else
use not allowed in expression at ./HB.pl line 13, at end of line
Execution of ./HB.pl aborted due to compilation errors.
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, #Donor, , Acceptor,
,
% Exist.);
for (my $o=1; $o=$nres; $o++) {
printf(OUT %10s\t%10s\t%10s\t%10s\t%10.3f\n, $donor_resn[$o],
$donor_names[$o], $acceptor_resn[$o], $acceptor_names[$o],
(($hbonds{$o}/$nframes)*100));
}
close(OUT);
exit;
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Dear Mark
I have a question as same as atila petrosian, but my system is protein-dna.
you said [IIRC g_select has some better documentation available once you run
it and ask for help, somewhat like make_ndx].
please explain IIRC more. Is IIRC a program or a list of archives?
any help will
Dear gromacs users
I was trying to count waters involved in the interface between Protein_A and
Protein_B.
I made a selection.dat file as follows:
waterO = group SOL and name OW;
heavy1 = group Protein_A and group Protein-H;
heavy2 = group Protein_B and group Protein-H;
inter = waterO and
integrase protein: a molecular dynamics analysis.
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Dear Mark
thanks for your attention.
I read manual before. I know that g_hbond is for hydrogen bond
analysis. But I don’t know about Van der Waals interactions analysis
and how to obtain percentage of them.
Please give me more information about what I said.
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- one to center the
peptide and one to group the waters in the same periodic cell as the
peptide.
I want to know how can I do last (group the waters in the same
periodic cell as the peptide)?
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Hi Carsten
Thanks for your answer. You got my case very well.
I understand your mean as follows:
1) Trjconv –f a.xtc –s a.tpr –o b.xtc –pbc mol (output group=water)
2) Trjconv –f a.xtc –s a.tpr –o c.xtc –pbc nojump (output group
=protein-dna)
Is that true?
You said, (Then
Dear Tsjerk
I did what you said:
1. trjconv -f a.xtc -s a.tpr -o 1.xtc -pbc nojump (system for output)
2. trjconv -f a.xtc -s a.tpr -o 2.xtc -pbc mol –center (pr/dna
for centering, system for output)
Now, I need new trajectory file for analysis. How I obtain new
trajectory file
Dear Carsten and David and Tsjerk
Thanks for your time and attention
My purpose of these questions is to find a way that 1) close two separated
strand of dna (in my case only –pbc nojump fix it) and also 2) water
molecules to be put in interface of between protein and dna. Because I want
to
Dear Tsjerk
Thus, as you said, Xtc file obtained from trjconv –pbc nojump only concerns
visualization. Thus, can I use old xtc file (with out –pbc nojump) for
analysis such as interfacial waters and water mediated hydrogen bonds or
every other analysis?
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Hi gromacs users
Since I study dynamic of interfacial water molecules between protein and
dna, I want to know, is there any keyword in gromacs to obtain number of
interfacial water molecules between protein and dna as a function of
simulation time? Is there any way which water molecules put in
Dear Mark
thanks for your attention
when I used trjconv -pbc nojump, I made one group (protein and dna) in index
file and I selected that as centering group.
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Dear Mark
my mean of [when I used trjconv -pbc nojump, I made one group (protein
and dna) in index file and I selected that as centering group.] is
that
the problem (nonentity of water molecules in interface of protein and
dna) was not solved.
what is your mean of [You might need two passes with
Dear Justin
thanks for your attention
in my case calcium ion is bonded to 4 oxygen atoms of C=O group of protein.
yes, Calcium ions are present in nearly all the force fields in Gromacs. but
there are only parameters in * nb.itp and not in * bon.itp. how to obtain
these new parameters for my
Dear Justin
Is there any way for this problem?
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Hi gromacs users
I want to study simulation of a protein including calcium ion. Can I use
gromacs force fields?
any help will highly appreciated.
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Dear mohsen ramezanpour* *
yes. calcium is a typical ligand in my pdb file.I used PRODRG server
to make topology file but
ERRDRG Too many atoms in this molecule (should be =300).
PRODRG Program terminated unsuccessfully, sorry!
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Dear mohsen ramezanpour
my pdb file has 3000atoms (protein) + 1 atom (calcium).
Should I separate ion from general pdb again?
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Dear gromacs users
I did simulation of protein-dna complex in a box with size 7,7,7. There are
5000 water molecule in this box. After full md simulation, I need a pdb or
gro file containing only water molecules being exactly environment of pr-dna
complex and not water molecules being in edges
Dear Erik Marklund
thabks for your attention
I want only have water molecules being in 1.5 nm of solute in final frame
(2 ps)
I used following command: trjorder -f *.xtc -s *.tpr -n *.ndx -o *.gro
-r 1.5 -b 2
is it true?
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Hi gromacs users
When I uesed command : trjconv -f com_full.xtc -s com_full.tpr -n com.ndx -o
com.xtc -pbc nojump -ur compact -center
gromacs gives me the following error:
Program trjconv, VERSION 4.0.5
Source code file: gmxfio.c, line: 609
Fatal error:
wrong string length 0 for string buf
Hi gromacs users
I obtained pdb input file for gromacs from STRAP program. this pdb
file coantains protein and dna. this pdb file was obtaind form
superposition of 2 other pdb files. there is one problem: when I see
pdb file obtained from STRAP program by VMD, some bonds are
disappeared whereas
Hi gromacs users
is there visual program other than VMD for seeing trajectory obtained from
gromacs?
thanks in advance.
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Hi gromacs users
I want to know what is purpose of -dt flag in most of commands? in my
analysis, different values for -dt
results in outcomes have not determined trend .
I used this flag for g_rms as follows :
if g_rms -f pr.xtc -s pr.tpr -n pr.ndx-o 5.xvg -dt 5 so :
gromacs record
Dear Vitaly Chaban
yes. my md simulation is equilibrioum.
I did simulation of protein-dna. I want to know how protein and dna close
together and interact together (approach of protein to major groove of dna).
thanks alot in advance.
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Hi all
pdb file for my protein was obtained by solution NMR. this file is as
follows :
ATOM 1 N GLY A 1 -25.349 -8.577 4.055 1.00 0.00
ATOM 2 CA GLY A 1 -24.037 -8.099 4.448 1.00 0.00
ATOM 3 C GLY A 1 -23.580 -6.913 3.622 1.00 0.00
ATOM
Hi gromacs users
in my system, there are pr, dna, water and Na and I want to obtain diffusion
of pr in dna but when I use g_msd command, gromacs says select only 1
group. should be this group pr or dna?
Thanks a lot in advance.
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Dear Mark Abraham
yes. pr means protein. I want to obtain diffusion of protein within dna. I
want to know how/how much pr diffuse to dna.
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Dear Mark Abraham
No, I want to measure something about the diffusion of my protein to
DNA (especially to major groove of DNA) in the presence of water (as
solvent).
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Dear Vitaly Chaban
I know using index file but gromacs say : select only 1 group. what is this
group ? protein? or DNA?
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Hi gromacs users
I did simulation of pr-dna by gromacs. I want to obtain diffusion coefficent
of pr to dna. I raed manual (g_msd) in which there are diffusion
coefficent only for 1 and 2 dimension as follows respectively :
-type : Compute diffusion coefficient in one direction: no, x, y or z
Hi all
how cgnr is determind in *.top file? based on?
Any help will highly appreciated!
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Dear Erik
thank for your answer.
my rtp file for amber 03 force field is as follow :
[ NGLY ]
[ atoms ]
Namber99_39 0.29430 1
H1amber99_17 0.16420 2
H2amber99_17 0.16420 3
H3amber99_17 0.16420 4
CAamber99_11 -0.01000 5
Dear Erik
you said Amber03 was not parameterized with charge groups and last column in
your rtp entry holds the chargegroup numbers. but
cgnr column in my top file does not looks just like it. in case of H1, H2
and H3.
* H1amber99_17 0.16420 2
** H2amber99_17 0.16420
Hi gromacs users
(1) Simulated annealing method is as two forms: single and periodic.
I want to do Simulated annealing for obtaining global minimum in protein
structure.
Which one of them is better? (in point of view obtaining to global minimum).
Thank you so much for any help!
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Hi gromacs users
I want to use simulated annealing. I have a question:
1) in mdp file, T-couple = no. is that true?
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Hi gromacs users
it is my mdp file:
annealing: single
annealing_npoints: 5
annealing_time: 0 3 6 9 12
annealing_temp: 500 450 400 350 300
300 is my ref-t. is it true?
Thank you so much for any help!
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Dear Justin
thanks for your attention
I want to use simulated annealing to obtain global minimum for protein-dna
structure. I will do first heating and then slowly cooling.
is my mdp file true, now?
T-couple = brendsen
ref-t = 300
annealing: single
annealing_npoints: 5
annealing_time: 0 3
Dear Justin
thanks for your accuracy.
I want to use simulated annealing to obtain global minimum for
protein-dna structure. I will do first heating and then slowly cooling and I
will my full md simulation in 300K. is my manner true?
if so, is my mdp file true, now?
Tcouple = berendsen
ref_t = 300
Hi
In hydrogen bond autocorrelation function c(t), correlation of what quantity
of hydrogen bond is considered?
thanks
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