doable. But do you think
simulating one protein without its neighbours could reflect its dynamics? Would
its boundary residues behave very differently compared to with neighbours?
-- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Wed, Apr
le for our university to provide.
-- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Tue, Apr 7, 2020 10:10 PM
To: "ZHANG
Cheng"<272699...@qq.com>;"gromacs.org_gmx-users"http://www.gromacs.org/Documentation/How-to
time is not reduced, as now only several
proteins are simulated. If I simulate all the several protein without any
fixing, I worry they will lose their conformation. So fixing the neighbours and
only focusing on the protein in the centre could be the solution.
-- Origin
It is a challenge to simulate the entire virus as it is too big and I do not
have such computational resources. So I was thinking to only simulate one coat
protein and its surrounding neighbours, but keep the neighbours relatively
fixed.
Can I ask
1) Is this a sensible idea to proceed?
2)
f time length"?
Thank you!
Yours sincerely
Cheng
-- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Wed, Apr 1, 2020 09:10 AM
To: "gromacs.org_gmx-users"http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
I am trying to compare trajectories from different MD simulations, including
different pH and different mutants. The initial PDB (i.e. 0.pdb) is the same,
but the derived PDBs (1.pdb, 2.pdb, etc.) are different due to protonation
states and mutations. Those different PDBs were used individually
Dear Gromacs,
There seems to be very little explanation on the "-surface" and "-output"
options of "gmx sasa":
-surface: This should always consist of all non-solvent atoms in the system.
The area of this group is always calculated
-output: can specify additional selections, which should be sub
Thank you Mark!
I have tried version 2019.3 as well.
Again, the manual input works all fine
https://github.com/lanselibai/gromacs-20200223/blob/master/manually_type
but the command using "echo" still had the same problem
https://github.com/lanselibai/gromacs-20200223/blob/master/echo
I also
gmx pdb2gmx, version 2020-beta2
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 130)
Fatal error:
Answer me for res GLUTAMINE 3!
-- Original ------
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Sat, Feb 22, 2020 04:39 AM
To: "g
I want to run more than 300 MD, each with a different PDB (more precisely,
variants derived from a same wild type). I need to manually assign the
protonation states using the "-inter" option every time, which is impossible
for more than 300 times.
gmx pdb2gmx -f protein.pdb -o protein_process
The "gmx mindist?? command can output the number of contacts (numcont) between
two groups as a function of time. Is there a way to only consider the native
contacts, without using the PLUMED?
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Li
I have gone through Mark Abraham's tutorial on REMD
http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B
Now I would like to run my own REMD, adjusted from Justin's Lysozyme tutorial
My purpose of running REMD is to generate sufficient conformation sampling, and
try to use them to explain the in vitro data at 65C (338.15K).
I am using the "Temperature generator for REMD-simulations" at
http://folding.bmc.uu.se/remd/
I am not sure about the "standard/default" values of sev
I am trying to follow the REMD from Mark Abraham at
http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B
At Stage 2, when I run the grompp command
(for dir in sim[0123]; do cd $dir; gm
pi -append" ?
-- Original ------
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Fri, Jan 17, 2020 00:57 AM
To: "gromacs.org_gmx-users"https://github.com/lanselibai/gromacs-20200116
The MD is run on our HPC cluster. So I personally could not compile it. I
/gromacs-20200116
The MD is run on our HPC cluster. So I personally could not compile it. Is
there still some way to get equivalent performance for the Version 2019?
-- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Thu, Jan 16, 2020 07:
Hi Justin, what kind of information should I look at in the log files? They are
too big to paste here. Would it be possible if you can see them
at https://github.com/lanselibai/gromacs-20200115 ;?
Thank you!
-- Original --
From: "ZHANG Cheng"<272
I have a nearly identical run using the "VERSION 2019.3" compared to my
previous "VERSION 5.1.1". Everything during the preparation is the same except
"-r" needs to be added in the "VERSION 2019.3". So "-r em.gro", "-r nvt.gro"
and "-r npt.gro" are added in the grompp commands for NVT, NPT and p
Thank you very much Paul, I got it!
-- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Mon, Nov 11, 2019 09:57 PM
To: "gromacs.org_gmx-users"http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Wo
Thank you Paul! I want to use more than one mpi processes for each of the REMD,
would it be possible?
-- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Mon, Nov 11, 2019 09:39 PM
To: "gromacs.org_gmx-users"http://www
I am using the same files based on Mark Abraham's REMD tutorial, except
using a recent Gromacs version
(gromacs/2019.3).http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B
For Stage
to make it correct?
-- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Sat, Nov 9, 2019 06:11 AM
To: "gromacs.org_gmx-users"http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read
Dear Sir or Madam,
I use this in my job.sh file:
#!/bin/bash -l
#$ -S /bin/bash
#$ -l h_rt=01:00:0
#$ -l mem=2G
#$ -l tmpfs=15G
#$ -N REMD
#$ -pe mpi 12
#$ -cwd
module load gcc-libs
module load compilers/intel/2018/update3
module load mpi/intel/2018/update3/intel
module load gromacs/2019.3
Dear All,
Due to a software that is only compatible to Version 3.3.1, I have to use that
to prepare the simulation box. I was told "command not found?? when using the
insert-molecules.
So what should I do to put multiple molecules in a box?
Thank you!
Cheng
--
Gromacs Users mailing list
I think it is a common practice to use RMSD increase to indicate the structure
deformation. And in many cases, this deformation is referred as unfolding.
But I think the RMSD increase could also come from collapse (i.e. shrinkage).
So would radius of gyration (Rg) be a better descriptor for un
--
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Wed, Feb 27, 2019 01:09 AM
To: "gromacs.org_gmx-users";"ZHANG
Cheng"<272699...@qq.com>;
Subject: Can I align individual domains (not the whole structure) in the RMSD?
My protein Fab has V
My protein Fab has VH, VL, CL, CH domains. Usually in the RMSD calculation, I
align the whole Fab first, then use a index file to calculate the domain's RMSD:
$ echo 1 19 | gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns -n
index.ndx
(Group 1 is the whole protein, Group 19 is one of
optimise the cpu and memory with the least queue
time.
Thank you!
-- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Tue, Feb 19, 2019 05:13 AM
To: "gromacs.org_gmx-users";
Subject: Is there a more efficient way to calcula
My coarse-grained system has 10 proteins, each has 442 residues. After a period
of time, those proteins aggregated. I want to use "gmx distance" to know which
residues most likely to involve contact with other proteins.
I prepared a index.ndx file, in which there are 442*442*(9+8+7 ... + 1) =
I think I know now:
gmx distance -f dynamic_noPBC.xtc -s dynamic -n index.ndx -select 'group 0 plus
group 1' -oall
-- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Sun, Feb 17, 2019 08:06 PM
To: "gromacs.org_gm
My gro file looks like this
$ Martini system from C226S.pdb
$ 72758
$ 1ASP BB1 15.982 3.547 3.592
$ 1ASPSC12 15.989 3.335 3.842
$ 2ILE BB3 15.668 3.625 3.593
$ 2ILESC14 15.538 3.345 3.620
$ 3GLN BB5 15.590 3.886
Dear Pedro Deira,
Sorry, could you please show me how to include the newline using "echo" with
only one command line?
Yours sincerely
Cheng
-- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Mon, Feb 11, 2019 06:36 AM
T
I can successfully output the index file by doing it step by step:
$ gmx make_ndx -f equilibration.gro
$ r 1-442
$ q
But I am not sure how to do it in just one line.
I tried these but all could not work
$ echo r 1-442 q | gmx make_ndx -f equilibration.gro
$ echo "r 1-442" q | gmx make_ndx -
Dear Gromacs friends,
I am trying to understand more on the "Steepest Descents" so that I can decide
if I need to better minimise the system by reducing the "emtol" or increasing
the "nsteps", or other ways.
The prompt is shown in the end. My understanding is, the algorithm randomly
chooses
I use these two lines to neutralise the system
$ gmx grompp -f minimization.mdp -r system-solvated.gro -c system-solvated.gro
-p system.top -o system_genion.tpr
$ echo W | gmx genion -s system_genion.tpr -o system_genion.gro -p system.top
-pname NA -nname CL -neutral -conc 0.2
(#include "mar
Dear martini friends,
(Sorry for still posting here as the martini forum does not get reply quickly)
I am evaluating which force field mostly suits my protein. From this link
http://www.cgmartini.nl/index.php/force-field-parameters/particle-definitions
there are 7 martini 2.x options to choose, 3
Dear Peter,
Thank you very much!
Yours sincerely
Cheng
-- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Fri, Feb 1, 2019 09:47 PM
To: "gromacs.org_gmx-users";
Subject: martini: what is the column position if "AS
Dear Martini users,
I want to change some chargeable residues into neutral forms. e.g. change "ASP"
to "ASP0".
If the column is indexed from 1 (not from 0), the "ASP" column positions are
21-23. So, if "ASP0" is used, should their column positions be 20-23 or 21-24
in the itp file?
Thank you
n shown in the generated itp file.
If "-merge" is missing, only the intra-chain SS bonds are shown in the
individual itp files.
So happy to see the martini forum come back!
Yours sincerely
Cheng
-- Original ------
From: "ZHANG Cheng"<2726
Dear Martini friends,
My protein has 10 Cys with 5 disulfind bonds in light chain (LC) and heavy
chain (HC):
) Interchain disulfide bond: LC214 ?C HC220
) Intrachain disulfide of LC: LC23 ?C LC88, LC134 ?C LC194
) Intrachain disulfide of HC: HC144 ?C HC200, HC96 ?C HC22
Using this command will
Dear Peter,
Thank you very much! I will use GLU0 and -nt.
Yours sincerely
Cheng
-- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Tue, Jan 29, 2019 08:38 AM
To: "gromacs.org_gmx-users";
Subject: How to adjust the def
Dear martini friends,
By default, the "martinize.py" will
1) for backbone atoms, positively charge the N-terminus (atom type Qd), and
negatively charge the C-terminus (atom type Qa).
2) for side chain chargeable residues, always positively charge the LYS and ARG
and negatively charge the A
Thank you very much Eric Smoll!
I will use "tc_grps = Protein Non-Protein".
-- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Mon, Jan 28, 2019 09:45 AM
To: "gromacs.org_gmx-users";
Subject: What is
In the mdp file, I am using "tcoupl = v-rescale".
Is there a difference between using "system" and separating groups for
"tc-grps"?
e.g.
; using "system":
tc-grps = system
tau-t= 1.0
ref-t= 335
; using separating groups:
tc-grps
box. Then fill the system with that minimised water
box. Problem solved!
Best
Cheng
-- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Tue, Jan 22, 2019 10:20 PM
To: "gromacs.org_gmx-users";
Subject: Re: Re: &quo
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:
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
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
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 is
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 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
Maxi
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 l
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: "
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"&
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
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
"-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-user
My backbone restraints is shown in the "Protein_A.itp" file:
#ifdef POSRES
#ifndef POSRES_FC
#define POSRES_FC 1000.00
#endif
[ position_restraints ]
11POSRES_FCPOSRES_FCPOSRES_FC
31POSRES_FCPOSRES_FCPOSRES_FC
51POSRES_FCPOSRES_FC
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!
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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
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.
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
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
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
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.
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
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
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
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
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
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,
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,
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,
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-
- 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
;
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..
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
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
- 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 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
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 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
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 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
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
.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,
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
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
?
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
--- 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
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
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,
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 ?
"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>;"
; 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 1
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 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
-- 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
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