Dear Gromacs,
I can think of different ways of running repeats, after reading Justin's
lysozyme tutorial.
The 1st way: all starting from the same em.tpr after energy minimization (EM)
and use em.tpr individually for subsequent steps (NVT, NPT and production MD):
) repeat 1: same em.tpr ?? NVT ?
t.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/07_equil2.html
Yours sincerely
Cheng
-- Original --
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Wed, Jan 10, 2018 09:11 PM
To: "gromacs.org_gmx-users";
Subject: What is the
Dear Gromacs,
This website can give us the Q(SASA), i.e. the fraction of SASA per residue,
with values from 0 to 1.
https://mathbio.crick.ac.uk/wiki/POPS
Can I ask if we can use "gmx sasa" to obtain similar information? I do not like
the "absolute" sasa, as it could not reflect the relative exp
--- Original ------
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Tue, Jan 16, 2018 02:50 AM
To: "gromacs.org_gmx-users";
Subject: Can I get the fraction of solvent accessible surface area using "gmx
sasa"?
Dear Gromacs,
This website can give us t
?
Thank you! So if I am using a index file, and the index 1 is the group I am
interested, should I use the below? What is the difference between "-output"
and "-o"?
echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -surface -output -n -o area.xvg -tu
ns
-- Origi
Hi Alexandr,
Thank you, but it is the same with spaces between |
:(
Cheng
-- Original --
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Tue, Jan 16, 2018 06:37 PM
To: "gromacs.org_gmx-users";
Subject: Re:Re: Can I get the frac
x sasa -f md_0_1.xtc -s md_0_1.tpr -n index_C226S.ndx -o area.xvg -tu
ns
I got:
0.0002.767
0.1002.757
0.2002.736
... ...
Do you know what is the meaning of the second column?
Thank you!
-- Original ------
From: "ZH
.901/2.736
... ...
-- Original --
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Tue, Jan 16, 2018 08:02 PM
To: "gromacs.org_gmx-users";
Subject: Re: Re:Can I get the fraction of solvent accessible surface area
using "gmx sasa"?
Hi Justin,
I got it, Thank you very much for all the help!
-- Original --
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Tue, Jan 16, 2018 08:46 PM
To: "gromacs.org_gmx-users";
Subject: Re: Re: Re:Can I get the fraction of solvent acce
Dear Gromacs,
I run Gromacs on our cluster, and use this command to continue my run from last
checkpoint.
gmx mdrun -deffnm md_0_1 -cpi -append
Each new run will generate four log files:
md_0_1.e
md_0_1.o
md_0_1.pe
md_0_1.po
Gradually, I have thousands of log files. So I used these comm
Thank you very much Justin! Sorry I did not realise that.
I will need to include an "except md_0_1.edr" in the deletion.
But does it correct that I can delete all the log files?
md_0_1.e
md_0_1.o
md_0_1.pe
md_0_1.po
-- Original --
From: &q
Dear Gromacs,
I am running MD at 500 K for my protein.
I used this to analyse the gyration radius
echo 1 | gmx gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvg
I thought the radius should keep increase, as the protein unfolds at high
temperature. However, all my repeats showed a droppin
Dear Gromacs,
Can I ask if there is an alternative to do_dssp for secondary structure
analysis?
I am waiting for our IT staff to install the DSSP on our cluster. But there was
some errors.
https://github.com/UCL-RITS/rcps-buildscripts/issues/137
While still waiting for that, can I ask if Grom
Dear Gromacs,
I have residue-based b-factor values for a protein. In the past, they were
assigned to the b-factor columns of pdb files. It would take a lot of space if
I extract all the pdb files. As the pdb files come from the xtc file, I wonder,
if I can modify the xtc file directly?
Thank y
- Original --
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Fri, Feb 2, 2018 04:44 AM
To: "gromacs.org_gmx-users";
Subject: Can I put b-factor into xtc file?
Dear Gromacs,
I have residue-based b-factor values for a protein. In the past, they were
assigned to t
Dear Gromacs,
I am using:
gmx editconf -f protein.pdb -bf bf.dat -o bf.pdb
to assign b-factor values to "protein.pdb", which contains multiple pdb frames.
However, the output "bf.pdb" only includes the first frame.
Can I ask is there a way to assign b-factor values to all the frames of one p
Dear Gromacs,
My protein only has 442 residues. After running
gmx do_dssp -f md_0_1_noPBC.xtc -s md_0_1.tpr -ssdump ssdump.dat -map ss.map -o
ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa averarea.xvg -tu ns
In the ss.xpm file, I got 443 numberings, i.e. y-axis is numbered from 1 to 44
;
Do you think the 443th line is the separator? So ignore the 443th line?
------ Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Thu, Feb 22, 2018 01:20 AM
To: "gromacs.org_gmx-users";"ZHANG
Cheng"<272699..
- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Thu, Feb 22, 2018 01:34 AM
To: "gromacs.org_gmx-users";
Subject: Re: Why "do_dssp" gives one more residue?
Dear Qinghua,
Yes, exactly! But the numbering is:
1-214: first chain
215-442: second chai
Dear Gromacs,
The scount.xvg file was obtained after running
echo 1 | gmx do_dssp -f md_0_1_noPBC.xtc -s md_0_1.tpr -ssdump ssdump.dat -map
ss.map -o ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa averarea.xvg
-tu ns
The secondary structures listed are:
'Structure','Coil','B-Sheet','B-
Dear Gromacs,
I use Command line:
gmx gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvg -tu ns
and was told:
Error in user input:
Invalid command-line options
Unknown command-line option -tu
So why "gyrate" could not be supplied with "-tu ns" option?
Thank you.
Yours sincer
Dear Gromacs,
In the ss.xpm file for secondary structures, can I ask if the first residue
shows first, or last residue shows first? Is this already written in the file?
I also have a chain separator. Can I ask does it show in the beginning or
between the two chains?
(Sorry, I asked this questi
Dear Gromacs,
(Sorry I post this again as I have not got confirmed answer yet)
In the ss.xpm file for secondary structures, can I ask if the first residue
shows first, or last residue shows first? I could not find the description in
the file.
I also have a chain separator. Can I ask does it s
Dear Gromacs,
I know I can see all the post from
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/
but can I search from this link? I do not want to download all of them to my PC.
Thank you.
Yours sincerely
Cheng
--
Gromacs Users mailing list
* Please search the archive at
http
I would like to share my answer for chain separator issue for the "gmx
do_dssp". Millions of thanks to Carsten!
The "gmx do_dssp" will output an additional line as chain separator between two
chains. We do NOT need to provide a "ss.map" file in our working directory, and
the command will find
0.5 0.5 0.5
= Chain_Separator 0.9 0.9 0.9
-- Original ------
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Fri, Apr 6, 2018 10:13 PM
To: "gromacs.org_gmx-users";"ZHANG
Cheng"<27269
Dear GROMACS users,
Can I ask a disulfide bond question if possible?
The link below is my protein L50K.pdb with 5 disulfide bonds.
https://copy.com/kPLlSianI4LtohNy
After using
gmx pdb2gmx -f L50K.pdb -o L50K_processed.gro -water spce -inter -ignh -merge
interactive
one of the disulfide
Dear GROMACS experts,
I am using pdb2gmx for a protein with 5 disulfind bond
https://copy.com/kPLlSianI4LtohNy
The distance between each Cys SG are: 0.203, 0.204, 0.204, 0.205, 0.167. As a
result, 10% margin of any value of the "reference length" in specbond.dat
cannot cover all of the 5 Cys
Dear GROMACS experts,
Can I ask is there a more efficient way to deal with the "-inter" option in the
pdb2gmx command?
Now, I have to manually assign individual protonation status one by one, which
takes a very long time. Sometimes I make a mistake and I have to re-do all of
them again.
Wou
Dear GROMACS,
Can I ask how to assign options of the same type?
For example, on the website of
http://manual.gromacs.org/current/programs/gmx-mdrun.html
It is said in the "Synopsis":
[-o [<.trr/.cpt/...>]
I want to name the output files as md.trr and md.cpt. However, the followings
do no
Dear GROMACS,
Can I ask how to extend my simulations? I would like to run a 50 ns job.
Because of the cluster limitation, I need to use several jobs to complete that.
##
Step1: grompp
After using "grompp" on
Dear GROMACS,
I am now using openmpi nodes to run GROMACS (e.g. mdrun_mpi) on our cluster.
When the nodes required are too many (e.g. more than 8), jobs always take a
long time to wait in the queue. So I wonder if there is a possibility that we
can
1) convert the job into many serial jobs?
2
Dear Gromacs expert,
I was trying to extend my simulations. Relevant files can be found at
https://copy.com/c8dDMnC0df2gbig9
To prepare the "md_0_1.tpr" file, I set the following in the "md_50ns.mdp" so
that it can run 50 ns in total.
nsteps = 2500
dt= 0.002
Then I submit the same
Dear GROMACS experts,
Can I ask if the following commandlines are correct for extending simulations?
gerun convert-tpr -s md_0_1.tpr -f md_0_1.trr -e md_0_1.edr -o md_0_1.tpr
gerun mdrun_mpi -deffnm md_0_1 -cpi md_0_1.cpt -maxh 0.5 -append
(My job.sh can be found at https://copy.com/lrFubrlq9
Dear GROMACS experts,
(Relevant files can be found on https://copy.com/7DMkn6OxJBqEZtqh)
I have been told in the error file:
... ...
Reading frame1700 time 17000.000
Reading frame1800 time 18000.000
Reading frame1900 time 19000.000
Reading frame2000 time 2.000
--
Dear GROMACS expert,
(Relevant files can be found at https://copy.com/7DMkn6OxJBqEZtqh)
I still encountered error of "Floating point exception(core dumped)" when
running "g_rms -s md_0_1.tpr -f md_0_1.xtc" on my Ubuntu. In the prompt, it
stopped and showed the error when it came to 20 ns:
..
Hi Justin,
Thank you for telling me the "gmx check" method. As I checked, it also shows
"Floating point exception(core dumped)" after 20 ns. So I think it is corrupt
as you have said. I will run it again.
Thank you very much.
Yours sincerely
Cheng
GROMACS: gmx check, VERSION 5.0.
Dear GROMACS researchers,
I was trying to assign the protonation status in one go by the following:
echo "15 y 1 1 1 .." | gmx pdb2gmx -f HC_A227E.pdb -o
HC_A227E_processed.gro -water spce -inter -ignh -merge interactive
In the commandline above, the ".." means the protonation status
Dear Gromacs,
I use "gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr"
to generate the tpr file on my own PC. Then I submitted it to our university
computer cluster, in which an older version is installed, and I got the Fatal
error:
Reading tpx file (md_0_1.tpr) version 1
Dear Gromacs,
I would like to extend my simulation.
200 ns was put in the "md.mdp" file, which was used to build "md_0_1.tpr".
Then, I use "mdrun -deffnm md_0_1" to submit "md_0_1.tpr".
Due to the limitation on our cluster, only 5 ns (for example) was simulated
when the job finishes. The "md_0_
is it for extending a completed job? In my case, I want to continue a
incompleted job.
Thank you.
Yours sincerely
Cheng
____
From: Zhang, Cheng
Sent: 29 December 2016 18:23
To: gromacs.org_gmx-users@maillist.sys.kth.se
Cc: Zhang, Cheng
Subject: How to extend my i
Hi Justin,
Thank you very much. It worked as you said [😊]
Yes, I was only using 10 min in the beginning, so no cpt file could be
generated.
Yours sincerely
Cheng
From: Zhang, Cheng
Sent: 29 December 2016 19:02:47
To: gromacs.org_gmx-users
Dear Gromacs users,
I got a list of errors after running "cmake ..". I am sure the "cmake" itself
is already installed. I am installing Gromacs 5.1.4 on ubuntu-14.04.1 on
VMwarePlayer on a Dell PC. Can I ask how to solve this?
Thank you.
Yours sincerely
Cheng
ucbepan@ubuntu:/mnt/hgfs/Docum
Dear Gromacs Researchers,
My old.mdp only sets 10 ns of simulation. Now it has finished, and I want to
extend it to 100 ns.
As shown on
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
Should I use the following two lines of code for the files in the same folder?
grompp -f
(Following Justin's suggestion)
Dear Gromacs Researchers,
My old.mdp only sets 10 ns of simulation. Now it has finished, and I want to
extend it to 100 ns.
As shown on
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
Should I use the following two lines of code for the fil
"gmx-users";
Subject: Re: [gmx-users] How to extend simulation?
On 4/3/17 2:07 PM, ZHANG Cheng wrote:
> (Following Justin's suggestion)
>
>
> Dear Gromacs Researchers,
> My old.mdp only sets 10 ns of simulation. Now it has finished, and I want to
> ex
Dear Gromacs Researchers,
Can I ask how to put excipients (e.g. sucrose, trehalose) into the simulation
box together with protein, salt and water? Those excipients do not strongly
interact with proteins, so they could not be treated as protein-ligand complex.
I learned how to prepare the prote
Dear Gromacs,
I am running Gromacs 5.0.4 on Ubuntu 14.04.1 LTS.
When I run "gmx view ..." as below:
gmx view -f dppc-md.xtc -s dppc-md.tpr
I got the following:
Compiled without X-Windows - can not run viewer.
Can I ask how to use "gmx view" on Ubuntu? Thank you.
Yours sincerely
Cheng
to contain CMakeLists.txt.
What I should do next?
Thank you.
Cheng
-- Original --
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Wed, May 10, 2017 02:58 AM
To: "gromacs.org_gmx-users";
Subject: How to use "gmx view" on
with the same issue "Compiled without X-Windows - can not run viewer."
) sudo apt-get install xorg-dev
) sudo apt-get install xorg-dev libglu1-mesa-dev
(Sorry, I am not sure how to find the files to download)
Thank you.
Yours sincerely
Cheng
-- Original ------
Dear Justin,
Thank you for your link. I know how to install the Gromacs based on your link.
But do you know where I can download the tar.gz file so that I can compile it
and then use "gmx view"?
Thank you.
Cheng
-- Original --
From: "ZHANG
- Original --
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Thu, May 11, 2017 02:50 AM
To: "gromacs.org_gmx-users";
Subject: Re: Re: Re: How to use "gmx view" on Ubuntu?
Dear Justin,
Thank you for your link. I know how to install the Gromac
help!
Yours sincerely
Cheng
-- Original ------
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Thu, May 11, 2017 04:27 AM
To: "gromacs.org_gmx-users";
Subject: Re: Re: Re: How to use "gmx view" on Ubuntu?
Dear Mark,
Yes, Justin gave me
Dear Gromacs,I am simulating pH 4 condition. I interactively assign the
protonation of chargeable residues of a protein based on PDB2PQR results by
setting pH=4 in the "pKa Options" (http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1/).
I do not add citrate or acetate molecules to the simulation box. So if
Dear Gromacs,
I got this fatal error after running "pdb2gmx":
Fatal error:
Residue 1 named ASP of a molecule in the input file was mapped
to an entry in the topology database, but the atom N used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fix
Dear Justin,
I replied the thread already, but it is waiting for approval due to large email
content. Could you please approve it?
Cheng
---Original---
From: "ZHANG Cheng"<272699...@qq.com>
Date: 2017/5/19 22:37:52
To: "gromacs.org_gmx-users";
Cc: "QQ"
Dear Justin,
The command line that got fatal error is:
gmx pdb2gmx -f HC_V215W.pdb -o HC_V215W_processed.gro -water spce -inter -ignh
-merge interactive
The command line that works fine is:
gmx pdb2gmx -f C226S.pdb -o C226S_processed.gro -water spce -inter -ignh -merge
interactive
(just change
Dear Gromacs,I have a protein PDB structure as well as its mutants PDB,
predicted by Rosetta with different ddG. After running pdb2gmx, I found that
the structures with lower ddG (more stable) all perform okay; while structures
with higher ddG (less stable) got fatal error:
Fatal error:
Residu
-- Original --
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Sat, May 20, 2017 09:32 PM
To: "gromacs.org_gmx-users";
Cc: "ZHANG Cheng"<272699...@qq.com>;
Subject: pdb2gmx do not work for unstable conformations
Dear Gromacs,I h
Dear Gromacs,
I am performing 370 K MD based on Justin's tutorial.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html
After "Step Five: Energy Minimization", I need to do NVT, NPT and a production
run.
I think I need to change 300 K to 370 K in three md
Dear Joao,
Sorry, I forgot. Thank you for reminding me. Is that all right now? Is that
true that NVT needs to change two lines, while NPT and production run only need
to change one line?
Yours sincerely
Cheng
1) In the NVT:
ref_t = 370 370 ; reference temperature, one for each grou
Dear Gromacs,
I did the below on Ubuntu 14.04:
tar xfz gromacs-5.1.4.tar.gz
cd gromacs-5.1.4
mkdir build
cd build
Then, I got error message when running:
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
The error log files can be found here:
https://1drv.ms/f/s!AjIs-W_id1LzobZfG
uot;mario";;
Date: Thu, Jun 1, 2017 02:44 PM
To: "gmx-users";
Cc: "gromacs.org_gmx-users"; "ZHANG
Cheng"<272699...@qq.com>;
Subject: Re: [gmx-users] "cmake" failed to install
Dear Cheng:
I solved that problem by following step by step instruc
Dear Mark and Mario,
Thank you very much. I delete the gromacs and redo the cmake and it works now.
Yours sincerely
Cheng
-- Original --
From: "mario";;
Date: Thu, Jun 1, 2017 04:07 PM
To: "ZHANG Cheng"<272699...@qq.com>;
Dear Gromacs,
I would like to simulate the protein at subzero condition in aqueous buffer, to
see if it becomes more stable than the elevated temperature (e.g. 65 C). Can I
ask what is the valid temperature range for water "spc216.gro" ? If I run the
simulation at -40 C, does it still assume the
and it outputs 10832 solvent molecules (i.e. water) after the
solvation step. So I assume "spc216.gro" refer to all the three-point water
models?
I am trying to see if my protein will be denatured in cold condition.
Yours sincerely
Cheng
-- Original -----
Dear Justin,
Thank you very much. I will try the possible water models.
Do you know if there are water models to resemble frozen state?
Yours sincerely
Cheng
-- Original --
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Thu, Jun 8, 2017 00:5
Dear Joao,
Thank you very much for your support. I am following Justin's tutorial but
simulating a fragment of antibody (Fab).
I will try the different water models.
Yours sincerely
Cheng
-- Original --
From: "ZHANG Cheng";<272699...@q
Dear Gromacs,
I try to use this command to calculate RMSF:
echo 3 | gmx rmsf -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsf_20-30ns.xvg -oq
bfac.pdb -res -b 2 -e 3
My simulation lasts for 30 ns, but I only want RMSF for the last 10 ns. It is
mandatory to assign a reference frame, so I use
Dear Gromacs,
I would like to perform simulations for a protein with glycines.
I think I should use "insert-molecules" as shown on
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/01_genconf.html
So I went to PRODRG2 Server to obtain the glycine structure by "tex
uot;gromacs.org_gmx-users";
Cc: "ZHANG Cheng"<272699...@qq.com>;
Subject: Re: [gmx-users] How to obtain a proper structure for glycine?
Hi,
Prodrg is not gromacs software, so there is probably a better place to ask this
question. I'd also look at their docs to find
3936GLY O19 0.047 -0.127
0.004 3936GLY O2 10 0.163 0.059 -0.0070.43801 0.27464
0.19713
-- Original --
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Mon, Aug 7, 2017 02:20 AM
To: "Mark Abraham";
&quo
Dear Gromacs,
I am doing a MD for a protein with glycines.
For glycine, I use
) gmx pdb2gmx -f gly_clean.pdb -o gly.gro -water spce -inter
and got
) gly.gro
) posre_gly.itp
) topol_gly.top
For protein, I use
) gmx pdb2gmx -f protein.pdb -o protein_processed.gro -water spce -inter -ignh
-merg
in_chain_L 1
into
[ molecules ]
; Compound#mols
Protein_chain_L 1 (the "Protein_chain_L" refers to the protein)
Protein 10 (the "Protein" refers to the glycine)
?
-- Original --
From:
Dear Gromacs,
I am trying to analyse my xtc file (40 ns) using:
echo 0|gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur
compact
However, it shows:
...
Fatal error:
Magic Number Error in XTC file (read 0, should be 1995)
...
Then I re-run the MD from the start from a sa
ion/Errors
---
-- Original --
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Sun, Aug 13, 2017 10:52 PM
To: "gromacs.org_gmx-users";
Cc: "ZHANG Cheng"<272699...@qq.com>;
Subject: Ma
filled with water and
NaCl.
-- Original --
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Mon, Aug 14, 2017 00:09 AM
To: "ZHANG Cheng"<272699...@qq.com>;
"gromacs.org_gmx-users";
Subject: Re: Magic Number Error
ask if the procedure is correct? Would you please recommend some tutorial
for prepare a system with protein and excipients (e.g. glycine, sorbitol, etc)?
Thank you.
-- Original --
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Mon, Aug 14, 2017 00:25 AM
T
Dear Gromacs,
My MD contains a protein (442 residues) and 203 free glycines. The numbering of
the residues is:
1-442: the protein residues
443-645: the 203 free glycines
When I use the "rms" command, all the 645 residues are considered as the
"Protein" category.
I cannot find an option that
Dear Gromacs,
After running
echo r 1-442 q|gmx make_ndx -f md_0_1.tpr -o index.ndx
I got a index.ndx file.
Then I run
echo 19 19|gmx rms -s md_0_1.tpr -f md_0_1.xtc -o rmsd.xvg -tu ns
But still only 18 options could be recognised. The index.ndx file is already in
the same folder.
So how to u
--- Original ------
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Mon, Aug 14, 2017 11:09 PM
To: "gromacs.org_gmx-users";
Cc: "ZHANG Cheng"<272699...@qq.com>;
Subject: How to use the index.ndx when running rms?
Dear Gromacs,
After r
--- Original ------
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Mon, Aug 14, 2017 11:50 PM
To: "ZHANG Cheng"<272699...@qq.com>;
"gromacs.org_gmx-users";
Subject: Re: How to use the index.ndx when running rms?
Hi Justin,
Thank you. I adde
Dear Gromacs,
After running
echo r 66 q|gmx make_ndx -f md_0_1.tpr -o index.ndx
I got the index.ndx file. However, all the sections are those default ones,
without the 66th residue atoms I want:
[ System ]
[ Protein ]
[ Protein-H ]
..
[ Ion ]
[ NA ]
[ CL ]
[ Water_and_ions ]
May I ask h
Dear Gromacs,
When I calculate the RMSD for the whole protein, I got values mostly from
0.2-0.5 nm. However, when I only calculate for a particular residue (using an
index file), the scale is mostly only 0.01-0.02 nm, even for a residue on the
loop.
My understanding is: when doing the RMSD, th
md_0_1_noPBC.xtc -n index.ndx -o rmsd.xvg -tu ns
2) Is there a tutorial/manual for using python to extract coordinates at
customised time and group?
I will look at the "gmx traj -ox".
Yours sincerely
Cheng
-- Original ------
From: "ZHANG Cheng&q
-- Original --
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Fri, Nov 24, 2017 06:25 PM
To: "gromacs.org_gmx-users";
Subject: Re: Does RMSD only consider the "relative" coordinate changes for the
selected group?
Dear Justin,
Thank you for con
Dear Gromacs,I am doing the RMSD calculation for a particular group of protein
residues. My system also has water molecules so there are more than 9
atoms. Thus, the 10th atom is indexed as 0, and 11th atom as 1, and so
on.
So if the index file for my group has an entry of 1, how c
t;;;
Date: Wed, Dec 6, 2017 04:34 AM
To: "gmx-users";
Cc: "gromacs.org_gmx-users"; "ZHANG
Cheng"<272699...@qq.com>;
Subject: Re: [gmx-users] How the index is recognised for values more than
9?
Hi,
The numbering of the coordinate file is not signi
Dear Gromacs,
I am following Justin's tutorial of "Lysozyme in Water" to run the MD.
The .trr file got more than 10 GB after 30 ns. So I plan to run a MD with less
frequent intervals.
In the md.mdp file, the "dt = 0.002". My understanding is to change the five
"5000" into "5" to achieve 1
; 3-D PBC
; Dispersion correction
DispCorr= EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no; Velocity generation is off
-- Original ------
From: "ZHANG Cheng";<272699...@qq.com>;
"compressed-x-grps=Protein" will set xtc-grps as a
group without waters and counterions?
------ Original --
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Fri, Dec 15, 2017 08:34 PM
To: "ZHANG
Cheng"<272699...@qq.com>;"
Dear Gromacs users,
In the pdb2gmx command, we are asked to select the force field to simulate our
protein system. I am told that a99SB-disp and CHARMM36m are better force-field
for the proteins. But both of them are not the default ones. Can I ask
1) What is the latest officical website to d
Thank you Justin. Do you know how to use the "define = -DUSE_OLD_C36" as shown
on
http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs
I want to make sure the CHARMM36m is used instead of CHARMM36.
-- Original --
From: "ZHANG Cheng&qu
Thank you very much! I got it now!
Cheng
-- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Sun, Dec 23, 2018 10:54 PM
To: "gromacs.org_gmx-users";
Subject: Re: How to install a new force-field?
Thank you Justin.
directory of $GMXLIB?
Thank you.
Cheng
-- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Sun, Dec 23, 2018 11:01 PM
To: "gromacs.org_gmx-users";
Subject: Re: Re: How to install a new force-field?
Thank you very m
I got the a99SB-disp forcefield with tip4pd.itp as the water model.
The a99SB-disp.ff file has been copied:
"/usr/local/gromacs/share/gromacs/top/a99SB-disp.ff"
The tip4pd.itp file has also been copied to
"/usr/local/gromacs/share/gromacs/top"
However using "-water tip4pd" in "pdb2gmx" will c
Thank you Justin.
The "watermodels.dat" and "tip4pd.itp" are already in the ff subdirectory.
The "watermodels.dat" content is:
tip4pd TIP4P-D TIP 4-point with increased dispersion
But "-water tip4pd" still has the error.
------ O
Invalid command-line options
In command-line option -water
Invalid value: tip4pd
-- Original ------
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Fri, Jan 11, 2019 00:31 AM
To: "gromacs.org_gmx-users";
Subject: Re: Why pdb2gmx could
Thank you Justin and Mark.
Using "-water select" works:
Select the Water Model:
1: TIP4P-D TIP 4-point with increased dispersion
2: None
-- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Fri, Jan 11, 2019 00:51 AM
T
I got the a99SBdisp force field with a tip4pd.itp water model. How can I
convert it to a tip4pd.gro file?
I need this water gro file for "gmx solvate".
Thank you!
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