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 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
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,
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 not
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?
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.
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 for
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
imulations,
but 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
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
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,
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
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
4, 2017 02:12 AM
To: "gmx-users"<gmx-us...@gromacs.org>;
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
(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
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
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
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"<gromacs.org_gmx-users@maillist.sy
Can I 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,
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
--- 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"<gromacs.org_gmx-users@maillist.sys.kth.se>;
Subject: Re: How to use the index.ndx whe
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
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 --
Fro
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"<mar
"gmx-users"<gmx-us...@gromacs.org>;
"gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>;
Cc: "ZHANG Cheng"<272699...@qq.com>;
Subject: Re: [gmx-users] How to obtain a proper structure for glycine?
Hi,
Prodrg is
help!
Yours sincerely
Cheng
-- Original ------
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Thu, May 11, 2017 04:27 AM
To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>;
Subject: Re: Re: Re: How to use "gmx vi
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 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
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"<gromacs.org_gmx-users@maillist.sys.kt
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
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
- Original --
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Thu, May 11, 2017 02:50 AM
To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>;
Subject: Re: Re: Re: How to use "gmx view" on Ubuntu?
Dear Justin,
Thank
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 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:
-- Original --
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Sat, May 20, 2017 09:32 PM
To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>;
Cc: "ZHANG Cheng"<272699...@qq.com>;
Subject: pdb2gmx do not work f
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
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
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
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...@qq.com
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";<ma...@exactas.unlpam.edu.ar>;
Date: Thu, Jun 1, 2017 04:07 PM
To: "ZHANG Cheng&qu
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:
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
-
From: "mario";<ma...@exactas.unlpam.edu.ar>;
Date: Thu, Jun 1, 2017 02:44 PM
To: "gmx-users"<gmx-us...@gromacs.org>;
Cc: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; "ZHANG
Cheng"<272699...@qq.com>;
Subject: Re: [gmx-use
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"<gromacs.org_gmx-u
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
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"<gromacs.org_gmx-users@maillist.sys.kth.se>;
Subject: Re: Does RMSD only consider the "relative" coordinate changes for the
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,
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
"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>;&quo
; 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>
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
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
m";<mark.j.abra...@gmail.com>;
Date: Wed, Dec 6, 2017 04:34 AM
To: "gmx-users"<gmx-us...@gromacs.org>;
Cc: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>; "ZHANG
Cheng"<272699...@qq.com>;
Subject: Re: [gmx-users] How th
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"<gromacs.or
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
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
--- Original ------
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Tue, Jan 16, 2018 02:50 AM
To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>;
Subject: Can I get the fraction of solvent accessible surface area using "gmx
sasa&quo
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"<gromacs.org_gmx-users@maillist.sys.kt
quot;?
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
-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: "ZHANG Cheng";<
.901/2.736
... ...
-- Original --
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Tue, Jan 16, 2018 08:02 PM
To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>;
Subject: Re: Re:Can I get the fraction of solvent accessible su
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
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
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"<gromacs.org_gmx-users@maillist.sys.kth.se>;
Subject: Re: Re
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
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
- Original --
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Fri, Feb 2, 2018 04:44 AM
To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>;
Subject: Can I put b-factor into xtc file?
Dear Gromacs,
I have residue-based b-factor va
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
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:
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
~~"
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"<gromacs.org_gmx-users@maillist.
- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Thu, Feb 22, 2018 01:34 AM
To: "gromacs.org_gmx-users"<gromacs.org_gmx-users@maillist.sys.kth.se>;
Subject: Re: Why "do_dssp" gives one more residue?
Dear Qinghua,
Yes, exactly! But the numb
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
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"<gromacs.org_gmx-users@mai
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
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
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
My understanding is, in the Gromacs 2018, we MUST use "-r target.pdb" to
replace the "define = -DPOSRES" option in the .mdp file.
However, how can I do position restraints only for certain atoms, e.g. only the
backbone atoms? I think, if I use "-r target.pdb", both the backbone and side
chain
on_restraints ]" section in the itp file
) the only difference is, add "-r target.gro" where the "target.gro" can be the
same as that for "-c" option.
Thank you very much!
Cheng
-- Original --
From: "ZHANG Cheng"&
Sorry for asking this. I now understand it.
See post at
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-January/123809.html
-- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Wed, Jan 16, 2019 04:27 AM
To: "
I am doing an energy minimization in a vacuum condition. There is no "emtol" in
the mdp file. The energy converges in the end, and tell me "Fmax < 10" as shown
below. So how this "< 10" is determined?
Steepest Descents converged to Fmax < 10 in 4063 steps
Potential Energy = -2.3973977e+04
Thank you so much, Justin and Mark!
-- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Fri, Jan 18, 2019 09:55 PM
To: "gromacs.org_gmx-users";
Subject: How the "Fmax" is determined without "emtol&
I use
gmx editconf -f protein.pdb -d 5 -bt dodecahedron -o protein.gro
to put the protein in a dodecahedron.
However, when I open the protein.gro in pymol, and type "show cell", only a
triclinic box is shown.
So how to visualise the dodecahedron in Pymol or VMD?
--
Gromacs Users mailing
In the command
gmx solvate -cp 128_minimized.gro -cs water.gro -o waterbox.gro -maxsol 768
-radius 0.21 -p dppc.top
768 waters are added, resulting in the "waterbox.gro".
However, the "dppc.top" is not updated for its "[ molecules ]" section. I can
of course manually add that. But why it
"-r 1UBQ-CG.pdb"?
So the whole command is the below?
gmx grompp -p system.top -r 1UBQ-CG.pdb -c solvated.gro -f minimization.mdp -o
minimization.tpr
------ Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Mon, Jan 14, 2019 10:16 PM
and the "Protein_A.itp" file has the restraints I need.
Should I modify the "minimization.mdp" instead?
-- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Mon, Jan 14, 2019 09:53 PM
To: "gromacs.org_gmx-u
In Gromacs 2018, -r is used to provide the restraint file for grompp.
I have a grompp command used for a coarse-grained (CG) gro file, i.e. CG.gro:
gmx grompp -f parameter.mdp -r AllAtom.pdb/CG.pdb -c CG.gro -p system.top -o
MD.tpr
So in the command above, should I use AllAtom.pdb or CG.pdb
I am doing coarse-grained (CG) modelling for 10 proteins in a box. I was told
"Too many LINCS warnings" in the minimization after solvation with
coarse-grained waters.
I try to diagnose the problems based on
http://manual.gromacs.org/documentation/2018/user-guide/terminology.html#blowing-up
am using this, but I do not know how to modify it.
https://github.com/lanselibai/martini/blob/master/20190121_LINCS/minimization_solvate.mdp
-- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Tue, Jan 22, 2019 00:12 AM
To: "gromacs.org_gmx
ential Energy = -2.4130119e+05
$ Maximum force = 9.1535597e+00 on atom 2335
$ Norm of force = 7.1063030e-01
Peter, how to replace all constraints for stiff bonds?
-- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date
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 Just
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
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
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