Dear All,
Will you please explain how the initial velocity may affect the MD results?
What the initial velocity really means? How the velocity of the atoms in the
protein changes in the MD process? What is the reasonable scope of the initial
velocity? Any suggestions on how to manually input a
http://www.rikgim.com/sq/ebetmmqleqljqo.ff
Acoot Brett
--
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uld extend it in picosecond (for example
> if you want to extend for 4ns you should put 4000).
>
> Cheers,
> EB
>
> -Original Message-
> From: gmx-users-boun...@gromacs.org
> [mailto:gmx-users-boun...@gromacs.org]
> On Behalf Of Acoot Brett
> Sent: Wednesday
Dear All,
I have run a 5 ns MD by
mdrun -deffnn md-0-1
After about 1 ns the computer was out of power by accident. I tried to continue
run the MD. From the on-line material there is a method "mdrun -s topol.tpr
-cpi state.cpt".
But by the above mdrun -deffnn md-0-1, I find I got 2 cpt files,
_hbond
> releases
> To: "Discussion list for GROMACS users"
> Received: Saturday, 24 November, 2012, 5:30 PM
> On 2012-11-24 05:41, Acoot Brett
> wrote:
> > If we got the results by 4.5.4, what will be the method
> to analyze it by 4.5.5? By a pathch or by installation
If we got the results by 4.5.4, what will be the method to analyze it by 4.5.5?
By a pathch or by installation of 4.5.5 to analyze the 4.5.4 results?
Cheers,
Acoot
--- On Sat, 24/11/12, Justin Lemkul wrote:
> From: Justin Lemkul
> Subject: Re: [gmx-users] Different average H bonds with diffe
Dear All
First I ran a 5 ns MD (md-0ns-5ns), I get md-0ns-5ns.tpr and
md-0ns-5ns.cpt,then I extend it for 1 ns by
tpbconv -s tpbconv -s md-0ns-5ns.tpr -extend 1000 -o md-5ns-to-6ns.tpr
mdrun -deffnm md-5ns-to-6ns -cpi md-0ns-5n.cpt
Then I further extend it for 2 ns by
tpbconv -s md-5ns-to-6
Dear All,
I have a protein composed of chain A and chain B. I want to determine the
interaction energy between chain A and chain B. Is it the following
energygrp_excl correct or not?
energygrp_excl=chain A chain A chain B chain B SOL SOL chain A SOL chain B SOL
Or is it tool long? I see from t
Dear All,
I have a protein complex PDB composed of chain A and Chain B. I want to
dtermine the hydrogen bonds between chain A and chain B.
By g_hbond it request me to input the group twice. But both chain A and chain B
belong to group "protein". In this situation how can I determine the hydroge
Dear All
First I ran a 5 ns MD (md-0ns-5ns), I get md-0ns-5ns.tpr and
md-0ns-5ns.cpt,then I extend it for 1 ns by
tpbconv -s tpbconv -s md-0ns-5ns.tpr -extend 1000 -o md-5ns-to-6ns.tpr
mdrun -deffnm md-5ns-to-6ns -cpi md-0ns-5n.cpt
Then I further extend it for 2 ns by
tpbconv -s md-5ns-to-6
Dear All,
for my original MD, based on mdp file the total time is 500 ps. After it
finished, I have decided to extend the MD run to 2.5 ns.
I think the following command should be used:
tpbconv -s original500ps.tpr -extend 2000 -o md-0.5ns-to-2.5ns.tpr
But as for in the original mdp file the
Dear All,
I just run a grompp command "grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p
topol.top -o npt.tpr". It gives the following message,
Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
Exc
-users] GROMACS command for energy calculation
On 27/08/2012 7:42 PM, Acoot Brett wrote:
> Dear Justin,
> For example, I want to calculate the energy between residue 50 and residue
>100, then I create an index file (A), then in the MDP file I will insert
>energygryp=A (with indec file
-
From: Justin Lemkul
To: Acoot Brett ; Discussion list for GROMACS users
Cc:
Sent: Monday, 27 August 2012 9:53 AM
Subject: Re: [gmx-users] GROMACS command for energy calculation
On 8/26/12 7:44 PM, Acoot Brett wrote:
> Dear All,
>
> I am still confused and I hope I can get some
] GROMACS command for energy calculation
On 27/08/2012 8:01 AM, Acoot Brett wrote:
> Dear Justin,
>
> In the internet there is the following content. But if I need to measure the
> non-bonded energy between residues within a protein, or between fragments
> within a protein, can yo
speeding up energy calculations with mdrun -rerun and for
excluding interactions within frozen groups.
- Original Message -
From: Justin Lemkul
To: Acoot Brett ; Discussion list for GROMACS users
Cc:
Sent: Monday, 27 August 2012 7:09 AM
Subject: Re: [gmx-users] GROMACS command for
Dear All,
After the production MD has been done, does GROMACS has a command which can
calculate the interaction energy between any 2 residues in a frame of structure
from the MD?
Cheers,
Acoot
--
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http://lists.gromacs.org/mailman/listinfo/gmx-
residue 1-40 in chain B by VMD, will you please advice a correct method?
Cheers,
Acoot
- Original Message -
From: Joaquim Rui de Castro Rodrigues
To: Acoot Brett ; Discussion list for GROMACS users
Cc:
Sent: Saturday, 18 August 2012 8:43 PM
Subject: RE: [gmx-users] 2 chain protein
Dear All,
After the production MD for a 2-chain protein complex (chain A and chain B) was
done, I used VMD to observe the trajectory. I want to color the 2 chains in
different color.
However it seems during the observation of the trajectory by VMD, VMD treated
both of the 2 chains as ch
,
Acoot
- Original Message -
From: Justin Lemkul
To: Acoot Brett ; Discussion list for GROMACS users
Cc:
Sent: Saturday, 18 August 2012 8:17 AM
Subject: Re: [gmx-users] xtc file and trr file
On 8/17/12 5:52 PM, Acoot Brett wrote:
> Dear Justin,
>
> But it is very dif
Dear Justin,
But it is very difficult to explain why the xtc file gives more frames in VMD
than trr file. Can you explain it? Or VMD has made the modification when read
the xtc file or the trr file?
Cheers,
Acoot
- Forwarded Message -
From: Justin Lemkul
To: Acoot Brett
: Discussion list for GROMACS users
Cc:
Sent: Friday, 17 August 2012 8:41 PM
Subject: Re: [gmx-users] xtc file and trr file
On 17/08/2012 6:46 PM, Acoot Brett wrote:
> Dear All,
>
> After a production MD, both the xtc file and trr file are produced. trr file
> is much larger than the xtc fi
Dear All,
After a production MD, both the xtc file and trr file are produced. trr file is
much larger than the xtc file. But when we openned the original gro file one of
the file from xtc file and trr file in VMD, we will find the xtc contains more
frames in comparison with the trr file.
Will
Dear All,
I just installed a VMD. And then I load a gro file and a xtc file from a
simulation. The bar in the VMD Main window continuously moves, however the
protein molecule in the OpenGL Display window does not move.
Will you please tell me what is the problem, or how can see the whole
sim
lle VIC 3010
> dallas.war...@monash.edu
> +61 3 9903 9304
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
>> -Original Message-
>> From: gmx-users-boun...@gromacs.org [mailto:gmx-user
Journals to me?
I am looking forward to getting your reply.
Cheers,
Acoot
- Original Message -
From: Albert
To: Acoot Brett ; Discussion list for GROMACS users
Cc:
Sent: Saturday, 11 August 2012 3:57 PM
Subject: Re: [gmx-users] a residue move in extremely large scale in MD
you have to
as a single step step?
Second, will you please tell me in " If the outcome of the analysis before and
after PBC correction are the same", which analysis can be used as the "outcome"
for the analysis?
Thanks.
Acoot
- Original Message -
From: Justin Lemkul
To: Ac
9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.
> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of Acoot Brett
> Sent: Wednesday, 8 Au
e VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.
> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of
-users] a residue move in extremely large scale in MD
On 6/08/2012 8:58 PM, Acoot Brett wrote:
> Dear All,
>
> I have a protein with about 400 amino acids. I have done a production MD of
> it. I find in the 400 amino acids, there is 1 amino acids, during the whole
> MD proces
Dear All,
I have a protein with about 400 amino acids. I have done a production MD of it.
I find in the 400 amino acids, there is 1 amino acids, during the whole MD
process, this residue moves in a extremely large scope in comparison with all
the other residues.
Do you think this single residu
Dear All,
Will you please tell me how to rename the C-terminal residue atom OXT so that
the OXT oxygen can be recognized by MOLMOL?
Cheers,
Acoot--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gr
your disposal.
I myself have not verified this, but colleagues have seen a good match between
the energy obtained from Espinoza's formula and the populations of HA-distances
in simulations.
Best,
Erik
3 jun 2012 kl. 10.23 skrev Acoot Brett:
Dear All,
>
>I want to know whether t
w they were derived.
>
> Good luck, your going to start seeing more and more a flood of biologist.
>
> Stephan Watkins
>
> Original-Nachricht
>> Datum: Thu, 31 May 2012 19:54:04 +1000
>> Von: Mark Abraham
>> An: Discussion list for GROMACS us
Dear All,
Can you tell me a web link on a protocol or reference for steered production MD
or the production MD just for only a fragment of the whole protein, by GROMACS?
Cheers,
Acoot--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Pleas
From: Mark Abraham
To: Discussion list for GROMACS users
Sent: Thursday, 31 May 2012 4:48 PM
Subject: Re: [gmx-users] How GROMACS calculate the energy of hydrogen bond
On 31/05/2012 4:42 PM, Acoot Brett wrote:
Dear All,
>The value of the energy of the hydro
Dear All,
The value of the energy of the hydrogen bond has relation with distance and
angle of the hydrogen bond related atoms. As for in the simulation process, the
distance and angle of the hydrogen bond related atoms may change continuously.
Will you please let me know based on which formula
Dear All,
Will you please tell me how GROMACS calculates the total charge of a protein at
pH 6.5? And how do we assign the ionization state of the residues, especially
for HIS at pH 6.5?
I am looking forward to getting a reply from you.
Cheers,
Acoot--
gmx-users mailing listgmx-users@gro
Dear All,
Will you please tell me a method or a server which can calculate the mean B
factor of all residues in a PDB file?
Cheers,
Acoot --
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs
Dear All,
By gromacs pdb2gmx, we can choose the amber force field. Suppose we have chosen
the amber force field, now let us see add ions.
By gromacs command "genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA
-nname CL -neutral -conc 0.1", besides neutralize the system, we also add 0
Dear All,
Before we run the production MD, we have minimized the energy and equilibriated
the system. Especially we will keep the temperature constant. Then which force
drive the protein to converge? Why the protein do not reverse its already
completed MD process before it converges, leading t
Dear All,
Before we run the production MD, we have minimized the energy and equilibriated
the system. Especially we will keep the temperature constant. Then which force
drive the protein to converge? Why the protein do not reverse its already
completed MD process before it converges, leading t
Dear All,
For the on-line tutorial of Justin Lemkul on NPT equilibriation
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/07_equil2.html),
if we extend the npt simulation time from 100 ps to 200 ps, is any possibility
that the black pressure curve would be smoo
In the on-line tutorial of Justin Lemkul
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html)
for both lysozyme, for the mini.mdp, nvt.mdp and npt.mdp, the nsteps
= 5. Do you think this valus is depend or independent of the molecular
weight of th
Dear All,
In the on-line tutorial of Justin Lemkul
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html)
for both lysozyme and the umbrella sampling, in the npt.mdp, there is
"tc-grps = Protein Non-Protein ; two coupling groups".
In the system of lysoz
Dear All,
The first mini.mdp is as following:
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent
minimization)
emtol = 1000.0; Sto
Dear All,
Suppose I have done a 5-ns production MD, I want to analysis the rmsd from 1 to
3 ns, will you please tell me the corresponding g_rms command?
Cheers,
Acoot--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the arch
Dear All,
I have a practice on the production MD according to the on-line lysozyme
tutorial of Justin Lemkul
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html).
By the production MD step, I got 2 .trr file, one is md_0_1.trr, the other is
traj.trr fil
for GROMACS users
Cc:
Sent: Saturday, 7 April 2012 11:58 AM
Subject: Re: [gmx-users] on PDB2gmx
On 2012-04-06 06:41:57PM -0700, Acoot Brett wrote:
> Dear All,
>
> Can I remove all the H from the PDB file and then input it to the pdb2gmx so
> that pdb2gmx can produce all the correct
Dear All,
Suppose in my PDB file for pdb2gmx I will include HISD, HISE, etc, will you
please tell me how to construct or find the the .rtp file? And the command to
use the .rtp file in the pdb2gmx?
Cheers,
Acoot
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mai
idines are usually neutral.
Francesco
Il 07/04/2012 09:42, Acoot Brett ha scritto:
> Dear All,
>
>I have a protein, the charged residue numbers in the protein is as following
>ARG 11
>ASP 19
>glu 25
>his 8
>lys 24
>
>asp+glu= 44
>arg+his+lys=43
>
>
Dear All,
I have a protein, the charged residue numbers in the protein is as following
ARG 11
ASP 19
glu 25
his 8
lys 24
asp+glu= 44
arg+his+lys=43
However the total charge of the protein given by pdb2gmx is -9.
Will you please introduce to me how pdb2gmx calculate the total charge
Dear All,
Can I remove all the H from the PDB file and then input it to the pdb2gmx so
that pdb2gmx can produce all the correct protonation state of the protein
residues including HIS?
Cheers,
Acoot --
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listi
Dear All,
For low resolution structure PDB, the protonation state of histidine is niot
clear. Then how does pdb2gmx treat the protonation state of HS?
Even for high resolution structure of protein, the protonation state of HIS is
usallly unclear or unspefified.
In the manual og gromacs,
Dear All,
Before and after extention we have 2 trajectorty files, and by trjcat we got
we, then we can do the g_rms
g_rms -s *.tpr -f *_noPBC.xtc -o rmsd.xvg -tu ns
But here for the g_rms command I find no matter whether we use the *.tpr of
the initiation of the production MD, or the *.tpr
do not use
append. It is the least confusing workflow to use.
On 2012-04-06 01:56:18PM +1000, Mark Abraham wrote:
> On 6/04/2012 1:41 PM, Acoot Brett wrote:
> > Dear All,
> > Frim mdrun -h, I got the following message:
> > /-[no]append bool yes Append to previous output files wh
Dear All,
Frim mdrun -h, I got the following message:
-[no]append bool yes Append to previous output files when continuing
from checkpoint instead of adding the simulation art number to all file names
Thus there is the possibility that the series xvg curves can never starts from
Dear All,
Have you paid attention to this fact, for some e-mails from our Discussion list
for GROMACS users, although they do not contain attachment files, the
attachment file symbols exist.
What is the reason?
Cheers,
Acoot --
gmx-users mailing listgmx-users@gromacs.org
http://lis
Hi Justin,
Can you give me your definition of converged MD and unconverged MD?
Cheers,
Acoot
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Friday, 6 April 2012 4:41 AM
Subject: Re: [gmx-users] Different results from identical tpr af
Here I want to talk on the time length of production MD.
I have a professor on computational biology. She said for MD only several ps is
enough. I have the expereince to run production MD for several ns, and I have
got stable conformation.
But I am sure for some protein system, even a 50 ns M
But we hope finally no matter which trajectory, a stable protein conformation
should be got! As for during the production MD, no significant energy change
included.
I am looking forward to getting more feedback on this topic.
Acoot
From: Peter C. Lai
To:
Dear All,
For pdb2gmx, we have -ignh. Does -ignh will always give the correct HIS format
at pH 7?
Looking forward to getting your reply.
Cheers,
Acoot
From: lina
To: Acoot Brett ; Discussion list for GROMACS users
Sent: Thursday, 5 April 2012 10:55
Dear All,
For the different protonation state of HIS, what are there 3-letter code for
GROMACS? And how about -SH and -S-S- codon? Or do you have a web link for me to
read? Do we still have any other confusing amino acids?
I am looking forward to getting a reply from you.
Cheers,
Acoot--
Dear All,
I have tried the MD command extension for several times, but for the series of
*.xvg curve analysis, it always comes from the time which the extension starts,
rather than the time where the original MD starts.
In order to decide whether we need to initiate the extension, we need do
Dear All,
In http://www-personal.umich.edu/~amadi/fwspidr_tutor.pdf, there is a command
tpbconv -f traj.trr -s topol.tpr -e ener.edr -o tpxout.tpr –until $VALUE
But we know we never have the topol.tpr as I know.
Will you please give a clarification?
Cheers,
Acoot --
gmx-users mailin
s,
Acoot
From: Mark Abraham
To: Discussion list for GROMACS users
Sent: Wednesday, 4 April 2012 6:56 PM
Subject: Re: [gmx-users] the -extend function of the tpbconv command
On 4/04/2012 6:24 PM, Acoot Brett wrote:
Hi Justin and All,
>
>The on
Dear All,
In the on-line tutorial on lysozyme
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/09_analysis.html),
there is a command
trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact
Will you please consider in that command whether
mdrun -s next.tpr -cpi
previous.cpt) is still unclear.
Will you please give an explaination?
Cheers,
Acoot
____
From: Justin A. Lemkul
To: Acoot Brett ; Discussion list for GROMACS users
Sent: Wednesday, 4 April 2012 10:36 AM
Subject: Re: [gmx-
method?
Cheers,
Acoot
From: Justin A. Lemkul
To: Acoot Brett ; Discussion list for GROMACS users
Sent: Tuesday, 3 April 2012 8:59 PM
Subject: Re: [gmx-users] on the Umbrella Sampling tutorial
Acoot Brett wrote:
>
> Dear All,
>
> For
Dear All,
I have completed a 1ns production MD. Then I intended to extend it for another
1 ns.
I use command
"tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi previous.cpt"
I think the results will be automatically attended to previous md_0_1.tpr and
md_0
Dear All,
For the on-line Umbrella Sampling tutorial
"http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/04_EM_equil.html";
of Justin Lemkul, will you pleasse tell me for the equilibration where there
is no NVT equilibration?
Cheers,
Acoot
--
gmx-users mailing
Dear All,
For the function of mdrun. will you please introduce
the time difference for the whole mdrun with or without "-v"? I suppose
with "-v" will need some calculation time, but I am not sure whether the
time spent is significant.
Cheers,
Acoot--
gmx-users mailing listgmx-users@gro
Dear All,
I planned to use the method introduced in the Umbrella Sampling on-line
tutorial of Justin Lemkul
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html).
But if a peptide is surrounded by a protein, which means the opening of the
protein-com
Dear All,
For gromcas 4.5.5 mdrun, is "-reprod (reproducibility)" is the default function
or not?
If not the default function, then how shod we input value for "-reprod" in
order to get high reproducibility? The value should be "yes" or "no"? The
on-line manual explanation on it makes me con
Dear All,
I planned to use the method introduced in the Umbrella Sampling on-line
tutorial of Justin Lemkul
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html).
But if a peptide is surrounded by a protein, which means the opening of the
protein-comple
Dear All,
I am raning the 100 ps npt according to the on-line tutorial. For the computer
reason it stops at about less than50 ps.
Then I$ tpbconv -s npt.tpr -until 100 -o 100npt.tpr
mdrun -s 100npt.tpr -cpi npt.cpt -v
After completes I analyzee the g-energy. But xgrace shows for pr
Hi Mark,
The fifth residue of Chain A is Asn, not Val. But Asn also no CG.
Acoot
From: Acoot Brett
To: Discussion list for GROMACS users
Sent: Monday, 2 April 2012 10:48 AM
Subject: Re: [gmx-users] pdb2gmx error
Hi Mark,
I have renumbered the
: Mark Abraham
To: Discussion list for GROMACS users
Sent: Monday, 2 April 2012 10:32 AM
Subject: Re: [gmx-users] pdb2gmx error
On 2/04/2012 10:26 AM, Acoot Brett wrote:
Hi Mark,
>
>As for the pdb2gmx is the first step, there is still no gro file and rtp file
>produced by this s
From: Mark Abraham
To: Discussion list for GROMACS users
Sent: Monday, 2 April 2012 10:22 AM
Subject: Re: [gmx-users] pdb2gmx error
On 2/04/2012 10:19 AM, Acoot Brett wrote:
Dear All,
>
>I just run a pdb2gmx of a protein, the error message is "
>Fatal err
Dear All,
I just run a pdb2gmx of a protein, the error message is "Fatal error:
Atom CG is used in an interaction of type atom in the topology
database, but an atom of that name was not found in residue
number 5."
According to the sugestion I have tried to find the reason in "
http://www.grom
Dear All,
Will you please tell me how different Groamcsr forcefields (including the AMBER
ones) treat the N-termijnal and C-terminal residues differently?
Cheers,
Acoot--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive
Sampling
Acoot Brett wrote:
> Thanks.
> The original PDB file (2BEG) has 5 chains. In your tutorial you fix chain B.
>Thus if I am right, the energy calculated should be the disintegation energy
>of the whole protein to the 5 chain peptide. In addition the protein chain in
>t
Discussion list for GROMACS users
Sent: Sunday, 1 April 2012 10:49 PM
Subject: Re: [gmx-users] on Umbrella Sampling
Acoot Brett wrote:
> Here I also mean how can I get the index.npt in the "grompp -f md_pull.mdp -c
> npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr"
Dear All,
In the on-line tutorial "Umbrella Sampling " byJustin Lemkul in
"http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html" ,
there is a command "grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx
-t npt.cpt -o pull.tpr". Here is the index.n
the gromacs calculation
On 1/04/2012 5:44 PM, Acoot Brett wrote:
Dear All,
>
>For the GROMACS 4.5.5, after installation the test link is unavaliable, thus
>we cannot run the test.
>
>For the AMBER, after we install it and run the test, although we can pass most
>of th
Dear All,
For the GROMACS 4.5.5, after installation the test link is unavaliable, thus we
cannot run the test.
For the AMBER, after we install it and run the test, although we can pass most
of the tests, we cannot pass all of the tests.
For GROMACS, can there anything wrong for the calculat
Dear All,
According to the lysozyme model in the tutorial of Justin Lemkul in
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html,
I am runing a 2 chain protein complex MD, and the steps are exactly same as in
that on-line tutorial except that I use the 2 chain pr
Dear All,
I remember before I have read a something on melting the protein from a
predefined starting temperature to a predefined end temperature by MD, so that
after the MD we can look at the whole process to see which part of the protein
unfold earlier, which part of the protein of the prote
Dear All,
There is a tutorial says the function of "-v" in mdrun is to make the md
process visible in the screen, which is correct.
However from the introduction of mdrun in the new version of gromacs, it says
the function of "-v" is to make "noisy and loud".
Will you please tell me what is th
Dear All,
What will be the difference for run regular production MD and non-equilibrium
MD? And website introduction?
Cheers,
Acoot--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support
Dear All,
Does anyone can make an introduction on the differences among the following
force fields for protein? Which are much easy to be accepted for publication
purpose?
Cheers,
Acoot
1: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
2: AMBER94 force field (Cornell
Dear All,
In "http://www.gromacs.org/Documentation/How-tos/REMD";, the first sentence is
"Replica-Exchange Molecular Dynamics (REMD) is a technique used to enhance
sampling relative to a standard molecular dynamics simulations by allowing
systems of similar potential energies to sample
confo
Dear All,
Can you show me a webpage to calculate the Tm (melting temperature) of a
protein (complex) by Gromacs?
Cheers,
Acoot
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
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Dear All,
Currently is it possible to run MD at a constant pH value?
I am looking forward to getting a reply from you.
Cheers,
Acoot
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Sup
Dear All,
During a 1 ns production analysis (before it completes), I can analysis the
RMSD by "g_rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns" without
influence the normal calculation of the production analysis, right?
Cheers,
Acoot --
gmx-users mailing listgmx-users@gr
Dear All,
Suppose I have run a 1 ns production MD. After analysis I find I need to run
another 1 ns production MD on the basis of the completed 1 ns MD.
In this way can the files by the second 2 ns production MD indicates the MD is
from 0 ns to 2 ns?
Cheers,
Acoot--
gmx-users mailing lis
Dear All,
For the npt.mdp downloaded from the Justin Lemkul tutorial, it seems we need to
add a line of "refcoord_scaling".
If so, its value should be "all" or "com"?
I am looking forward to getting a reply from you.
Cheers,
Acoot --
gmx-users mailing listgmx-users@gromacs.org
htt
Dear All,
Suppose I have a 5 ns productive MD, will you please tell me the command to
extract the PDB file at exactly 3.5 ns?
Cheers,
Acoot--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.
older
and paste it into the gromacs running folder, in cygwin gromcas the pab can be
read (or can be open by vi).
But there is still ununderstandable why by cp the pdb file is not permitted to
open.
Cheers,
Acoot
From: Tsjerk Wassenaar
To: Acoot Brett ;
Dear All,
I am running energy minimization "mdrun -v -deffnm em". The number of atoms in
my system is far more than 4018, especially after the water box edded.
However in the "mdrun -v -deffnm em" running process, the screen shows "Step=
816, Dmax= 1.9e-02 nm, Epot= -3.04546e+06 Fmax= 1.5493
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