input.
The latter gives values of better sense from my actual example.
Sincerely,
Pengzhi
On 2/11/13 5:26 PM, Pengzhi Zhang wrote:
> Justin, I'm a little confused again. Let me put it in a more general
> way. If I used everything in .pdb and .trr files in reduced units
> {\sigma}
ut is
{\sigma}*10. Is it correct?
Sincerely,
Pengzhi
On 2/11/13 5:02 PM, Pengzhi Zhang wrote:
> Thanks Justin.
>
> I do use a .pdb file as the topology file, which is also in Angstrom,
> not in full format of pdb though (basically atom index ,name and
> coordinates). So in my case, g
understand it correctly?
Sincerely,
Pengzhi
On 2/11/13 4:09 PM, Pengzhi Zhang wrote:
> Hello there,
>
> I'm a gromacs newbie. I am using gromacs function g_anaeig to do
> principle component analysis. I use coordinates (converted to be .trr
> files for
> gromacs) and topology
Hello there,
I'm a gromacs newbie. I am using gromacs function g_anaeig to do principle
component analysis. I use coordinates (converted to be .trr files for
gromacs) and topology from amber. I know that gromacs works with units like
nm, kJ/mol etc, while amber with angstrom. Does anyone know tha
appreciate your
valuable suggestion.
Best Regards,
Rui
On Sat, Feb 2, 2013 at 1:34 PM, Justin Lemkul wrote:
>
>
> On 2/2/13 9:30 AM, Rui Zhang wrote:
>
>> Dear all,
>> Could anyone help me on my previous questions? Please reply me... (I know
>> it might be a ha
gards,
Rui
On Fri, Feb 1, 2013 at 10:49 AM, Rui Zhang wrote:
> Hello,
>
> I want to derive the atomic partial charges for heme in chloroperoxidase,
> since these parameters cannot be found in the GROMOS53a6 force field.
> Chloroperoxidase is a cysteine-ligated heme protein (high sp
Hello,
I want to derive the atomic partial charges for heme in chloroperoxidase,
since these parameters cannot be found in the GROMOS53a6 force field.
Chloroperoxidase is a cysteine-ligated heme protein (high spin) much like
P450. In my work, I want to study the interactions between the protein
re
Dear gromacs users,
We just published a paper titled "Force field development for cofactors
in the photosystem II" in Journal of Computational Chemistry, which
includes the Amber03 compatible force field for heme-B and works well
with heme proteins. You may use it for reference at your convenienc
lready finished any
tasks with this wall algorithm, can you kindly attach your topology files
to me?
Soo many thanks!!!!!
--
Huaichen(Bobby) ZHANG
+31 648478172
MSc Sustainable Energy Engineering
Royal Institute of Technology (Sweden)
Eindhoven University of Techno
un" (hostlist file as
follows), the same message as above appeared.
"
node018 slots=8
node022 slots=8
"
While the same commands works well for other softwares. Have anyone
encountered similar problem? What is your solution?
Thanks in advance!
--
Huaichen(Bobby) ZHANG
+31 64847817
Hi, ALL
Has anyone heard that there has been a bug in the energy calculation
of TIP4P water in older GROMACS (from v3.3 to v4.0.5) ?
Thanks !
Guozhen
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Please search the archive at
htt
Hi, ALL
We are writing our own MD program to simulate water and the TIP4P model
is being considered.
I am wondering that how does GROMACS program handle the force on the
massless M site of the TIP4P
model? It would be better to be informed the algorithm(or the code in
GROMACS). Thanks.
Gu
Dear Justin and Mark：
Thank you for your kind help！I think I figure out the problem
Best Regards
rtzhang
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Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search befo
Dear gmxusers.
I have problems about temperature coupling. Here is my parameter for
temperature coupling.
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tc-grps = System
tau_t = 0.1
ref_t = 298
I used "g_traj -f t
I have been performing MD simulation on electrolyte solution recently. And I
want to calculate the dipoles between cation-anion pairs. But I have no clue
how to achieve this by gromacs. I also want to know the algorithm for command
"g_dipole" about how to cheat a system with both molecules and i
is actually read by gromacs program ?
Thanks,
Guozhen Zhang
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Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't
Dear man or madam,
I have a question about the dihedral types in the topology.
If I made the topology by hand, is it possible to combine the type 9
and type 3 for proper dihedrals? Any comment about that?
Thanks.
Best,
Lu
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gmx-users mailing listgmx-users@gromacs.org
http://lists.g
Hi, ALL
I met a bizarre in a NVT simulation in which the initial temperature is
ridiculously high.
Even though I specify the initial temperature to be 200 K.
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = yes
gen_temp = 200.0
gen_seed = 173529
En
late crystals in Gromacs
From:"Mark Abraham"
Date:Thu, April 7, 2011 12:05 pm
To: "Discussion list for GROMACS users"
------
On 7/04/2011 1:55 PM, ZHANG Lu wrote:
> Dear all,
>I am
Dear all,
I am now trying to simulate crystals in Gromacs.
What I did was to convert the original crystal structure in cif format
to pdb format and then use genconf to replicate the cells and run MD.
Is it proper to do it in this way? Because the structure I got after MD
run was completely
Dear all,
I am now developing a set of force field parameters and I want to
calculate the spectral density with the normal mode analysis in GROMACS
to check my parameters.
The point here is that I want to get a plot (spectral density VS
frequencies). Could anybody give me some slides or tutor
Hi Mark,
Your analyses are
quite reasonable. The low-temperature replicas are indeed doing much more work
than the high-temperature replicas. As you said, the lowest temperature replica
in the 24-replica should take an amount of time comparable to that of the
lowest in the 42-replica. So for
nergies 4 442 28.722 13.7
0.3
Rest 4 8426.029 4012.4
96.6
---
Total 4 8726.270 4155.4
100.0
Qiong
On 7/02/201
Dear all gmx-users,
I have recently been testing the REMD
simulations. I was running simulations on a supercomputer system based
on the AMD Opteron 12-core (2.1 GHz) processors. The Gromacs 4.5.3
version was used.
I have a system of 5172 atoms, of which 138
atoms belong to solute and the
5756
0.211.7966 10.2602 17.5768
0.411.7928 10.2594 17.5783
0.611.789 10.2582 17.5799
0.811.7856 10.2552 17.5817
1 11.7831 10.2547 17.5837
1.211.7828 10.2554 17.586
1.411.7846 10.2562 17.5884
1.6 11.7891 10.2582 17.5909
1.811.7942 10.2621 17.5934
Best
Hi, ALL
I'm using "genbox" to create a water box. There is a flag called
"-nice" which is described to be used to set the nicelevel.
What is nicelevel ? What does the default value "19" mean ? What if I would
like to increase the decimal places (the default
is 3) of all numbers. Thanks.
rotein and none of them give me sensible
results (the charges are not all set to zero). Is this supposed to be
a bug?
Thanks,
Bin
On 2010-12-03 08.45, BIN ZHANG wrote:
Hi, all:
I was trying to use "tpbconv" to modify the tpr file with the
command:
tpbconv -s %s.tpr -nsteps -
Hi, all:
I was trying to use "tpbconv" to modify the tpr file with the command:
tpbconv -s %s.tpr -nsteps -1 -zeroq -n index -o final.tpr
It basically sets the charge of one group to zero. However, when I
perform mdrun -rerun, all the coulombic energies are zeros, i.e.,
Coulomb-(SR), Coul.-r
Dear all:
I used gromacs 4.5.2 to generate the topology for a small protein with
charmm27.
pdb2gmx_mpi -f 1PIN.pdb -o protein.gro -vsite hydrogen -his -ignh -ter
-p topol -nochargegrp
When I try to use the topology in grompp, the following error appeared:
Fatal error:
Can't do GB electrosta
BUILD_SHARED_LIBS and or you can ran "make
install" as a workaround until the bug is fixed.
Roland
On Tue, Sep 28, 2010 at 3:02 AM, BIN ZHANG wrote:
Hi, there:
I was trying to compile gromacs4.5.1 on a GPU cluster (https://secure.nersc.gov/nusers/systems/dirac/
).
The compilation see
Hi, there:
I was trying to compile gromacs4.5.1 on a GPU cluster (https://secure.nersc.gov/nusers/systems/dirac/
).
The compilation seems to work fine, but in the installation folder,
only "bin/mdrun-gpu" presents. Is it supposed to be so?
When I type "./mdrun-gpu -h", the following error
Dear Justin:
Thanks a lot for your reply.
I indeed have missing residues in the second chain. However, when I
try pdb2gmx -renum, it renumbers the second chain starting from 1,
rather than starting from 817(Nres_1st+1).
Thanks,
Bin
=
816VAL HG131
Hi, there:
I found that in gromacs version 4.5.1, the residue ids are not ordered
consecutively as before in the .gro file. For example, if I have two
chains in the protein, then the residue ids will be ordered with
respect to each individual chain, rather than reordered to be a
complete
work?
cheers
xiaohua
On Mon, Sep 20, 2010 at 10:04 AM, Justin A. Lemkul wrote:
>
>
> Xiaohua Zhang wrote:
>
>> Dear gmx-users
>>
>> I want to design such kind of computer experiment:
>>
>> For a system composed of non-bonded three layers (carbon nanot
unit kJ mol-1 nm-1
but how about group1 ?
Could you give me some suggestion?
cheers
xiaohua
--
Xiaohua Zhang
Suzhou Institute of Nano-Tech and Nano-Bionics
Ruoshui Road 398, Suzhou 215123, China
Phone: +86 512 62872552
Mobile: +86 137 71904040
Email: zhan...@fudan.edu.cn
Email: xhzhang2
Hi, there:
It seems to me that there was a bug at line 214 of function
read_next_vmd_frame() in file ./src/gmxlib/vmdio.c.
vec[0] = .1*ts.A; vec[1] = .1*ts.B; vec[2] = .1*ts.B; should be
changed to :
vec[0] = .1*ts.A; vec[1] = .1*ts.B; vec[2] = .1*ts.C;
This is identified in gromacs4.5.1 ve
noted.
There can be many reasons for your seg. fault, however.
Did you do energy minimization before starting md?
Please also test the same system with using a cut-off to see if that
works.
/Per
8 aug 2010 kl. 22.36 skrev BIN ZHANG:
> But the problem is with this set up, I will always
Dear all:
I have a question about the appropriate cut-off usage in implicit
solvent simulation. After googling for a while, I found most
references mentioning using non cut-off for these type of simulations.
For non cut-off, I assume in gromacs using the following parameters:
coulombtype
You can use the command trjconv to obtain them.
trjconv -s md -f md -dt 1000 -o out.pdb
For more information, please see the help of trjconv.
Zhang Cun
> Message: 7
> Date: Fri, 16 Jul 2010 12:32:36 +0530 (IST)
> From: sonali dhindwal
> Subject: [gmx-users] to visualise protein
MX?
Thank you!
Yours,
Zhang Cun
The main mdp parameters is as follow:
dt = 0.0005
energygrps = CNT GRA
; CNT is the group of Carbon Nanotube,GRA is the group of graphite
vdw-type = Cut-off
rvdw= 1
yce/amber#cof
However, I would also ask is there a specific reason you wish to use
OPLS-AA/L? If not then it is probably easier to use one of the AMBER
forcefields with these parameters as you do not need to do any
testing (or wait for me to publish my work!)
Cheers
Tom
BIN ZHANG wrote:
Hi,
I recently made up a topology for ADP. You can probably modify it to
ATP easily.
I used native OPLS atom types based on the DNA parameters (http://rnp-group.genebee.msu.su/3d/ff.htm
). The charges are copied from CHARMM27. Also, there is one dihedral
angle missing, again, copied from CHA
Dear all:
I'm considering to convert the ATP/ADP parameters from amber (http://www.pharmacy.manchester.ac.uk/bryce/amber
) into OPLS format. My question is, have you guys done similar things?
If so, can you give me some information on what kind of thing I should
be aware of? Like the scaling
Dear all:
I know this question has been asked many times, but it's still
tempting for me to ask it again ;-). Could any one suggest a mdp file,
including the proper parameter setting, for implicit solvent
simulation in gromacs? From all the clues I gathered (the roadmap, the
source code),
Justin,
Yes,it's fixed. Thank you.
Zhang Cun
> Message: 1
> Date: Mon, 17 May 2010 07:15:31 -0400
> From: "Justin A. Lemkul"
> Subject: Re: [gmx-users] About wiki error
> To: Discussion list for GROMACS users
> Message-ID: <4bf12553.2070...@vt.edu>
>
Hi, there seems two errors in the following page:
http://www.gromacs.org/Documentation/Terminology/NVT say NVT is
microcanonical ensemble.
and
http://www.gromacs.org/Documentation/Terminology/NVE say NVE is
canonical ensemble.
I register at wiki, but haven't authority to modify them.
Can anybo
downloaded
from the GROMACS website:
http://www.gromacs.org/index.php?title=Download_%26_Installation
Roland
On Mon, May 10, 2010 at 1:42 PM, BIN ZHANG wrote:
Dear all:
I found this really interesting email on the mail list about the
python wrapper for the xdrfile library:
http
Dear all:
I found this really interesting email on the mail list about the
python wrapper for the xdrfile library:
http://oldwww.gromacs.org/pipermail/gmx-developers/2009-March/003176.html
But unfortunately the link for the python files are not valid anymore.
I am wondering whether this proj
Dear Chris:
Thanks very much for the info.
I will take a look at the source code and see how far I can go.;-)
Bin
On Apr 9, 2010, at 11:38 AM, chris.ne...@utoronto.ca wrote:
Dear Bin:
What you request is not currently possible with any distribution up
to gmx-4.0.7 (I don't know if it is i
Dear all:
Reading about the gromacs4 manual, I couldn't figure out a way to
apply two sets of pulling simultaneously in gromacs?
I know you can specify a second group using pull_group2, but it has to
use the same reference group in pull_group0, correct? Then I don't
understand how one can a
Dear Mark:
Thanks a lot for all the suggestions. They are really illuminating.
Sincerely,
Bin
On Mar 26, 2010, at 5:56 PM, Mark Abraham wrote:
On 27/03/2010 8:24 AM, BIN ZHANG wrote:
Dear all:
In gromacs, is it possible to output forces between two groups of
atoms?
Yes. Run a
Dear all:
In gromacs, is it possible to output forces between two groups of
atoms? Or is it possible to decompose forces into separate parts, like
for LJ, and electrostatics?
Thanks,
Bin
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gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
(there were problems
with Gromacs and PGI before).
Roland
On Wed, Mar 17, 2010 at 1:27 PM, BIN ZHANG wrote:
Dear mark, and Roland:
Thanks for all the suggestions.
I was confused gromacs4 paper with another one by Erik Lindahl. (http://www.ncbi.nlm.nih.gov/pubmed/19229308
) Since there the
benckmark, on
a cray-xt4 machine. Here is also a link for the machine I'm working
on: http://www.nersc.gov/nusers/systems/franklin/
Bin.
On Mar 17, 2010, at 1:39 AM, Roland Schulz wrote:
On Wed, Mar 17, 2010 at 3:55 AM, Mark Abraham
wrote:
On 17/03/2010 6:19 PM, BIN ZHANG wrote:
protein and I'm using berger lipid/OPLS-AA
force filed.
Thanks
Bin
On Mar 17, 2010, at 12:02 AM, Mark Abraham wrote:
On 17/03/2010 5:43 PM, BIN ZHANG wrote:
Dear all:
I was trying to build gromacs 4.0 on a cray-xt4 machine, the same
one as
the benchmark in the gromacs4 paper (). Howe
Dear all:
I was trying to build gromacs 4.0 on a cray-xt4 machine, the same one
as the benchmark in the gromacs4 paper (). However, my timing for a
similar system, ~100,000 atoms, is almost 3 times slower than in the
paper. For example, I only got ~25 ns/day with 128 cpus. So is there
any
Dear Chris:
Now it makes all sense. Thanks a lot.
And your method surly works great.
Bin
On Mar 15, 2010, at 9:23 AM, chris.ne...@utoronto.ca wrote:
Dear Bin,
I think that you are getting confused here between different
publications. It was the Lindahl, E., and O. Edholm. 2000. paper
tha
Dear Chris:
Thanks a lot for your reply. That's really helpful. Now I have a
further question:
"1,4 electrostatic inter-actions were reduced a factor of 2 and 1,4
Lennard?Jones interactions a factor of 8."
I can understand that the LJ1-4 can be reduced by simply scale epsilon
in [pairty
Dear all:
I was trying to convert the lipid.itp downloaded from Tieleman's
website to the format compatible with OPLS. I basically followed the
procedure in this post, which is really helpful:
http://www.mail-archive.com/gmx-users@gromacs.org/msg03459.html
But there is one comment there I d
the interaction energy
(E_inter = E_(1+2) - E_1 - E_2). They also used PME to deal with the long range
electrostatic interaction. The force field they used is charmm.
Any advice or comment are welcome!
Thank you very much in advance.
Qiong
On 10/03/2010 7:56 AM, Qiong Zhang wrote:
Hi dear Mark
ot be decomposed group-wise." Maybe a better way
to overcome this is using the formula:
E_interact=E_tot(1-2)-E_tot(1)-E_tot(2)
Do you agree with this?
I am highly appreciative for all your help!
Qiong
On 9/03/2010 9:32 PM, Qiong Zhang wrote:
Hi gmx users,
I found the big discrepancy b
?
Thank you very much!
Qiong
[gmx-users] Re:problem with interaction energy calculated byg_energy
Qiong Zhang
Tue, 09 Mar 2010 01:17:02 -0800
Hi dear Mark,
Please ignor my last mail replied to you. I made some mistake
you use
in such interaction energy calculations?
Thank you very much!
Qiong
--- On Tue, 3/9/10, Qiong Zhang
wrote:
From: Qiong Zhang
Subject: Re:problem with interaction energy calculated by g_energy
To: gmx-users@gromacs.org
Date: Tuesday, March 9, 2010, 4:27 PM
Hi dea
e excluded.
Am I right here?
For the second summing up problem, I am still checking all the input file,
especially the index file.
Thank you very much!
Qiong
- Original Message -
From: Qiong Zhang
Date: Monday, March 8, 2010 20:35
Subject: [gmx-users] problem with interaction energy ca
Dear gmx users,
I am studying the adsorption behavior of a molecule ( molecule 1) on a surface
(molecules 2). Based on the production run, I calculated the interaction energy
between molecule 1 and molecules 2 by g_energy.
Here comes the first question: Why only short range interactions between
You may first use make_ndx to create the index file then use trjconv to save
the sub-system.
On Jan 12, 2010, at 7:14 PM, zh.li wrote:
> Dear all,
>
> I want to remove the water molecules in the original traj file (run.xtc)
> to save the space, so that I should use the command “trjconv”.
Dear GMX-Users,
I'm testing my 256 full hydrated lipid on blue gene. The purpose is to find out
the right number for "-npme", as mdrun can not estimate itself successfully.
I met the problem that how to match the maxinum allowed number for DD cells
with large number of CPU cores.
My simulation
Hi, All
Given the configuration file of a bulk SPCE water system, how can I add
a Na+ and Cl- into it using some gromacs or vmd tool? I tried autoionize
tool in vmd, but failed due to no psf file; then I tried autopsfgen tool,
failed again due to no proper topology file that can recognize SPC
script.
I will read the doucment you mentioned carefully .
And I will fix these notes and warnings as grompp and mdrun suggest.
Thank you for your help !
Cun Zhang
> Again, heed the note. I cannot think of a solid reason for a modern
> simulation
> being conducted using cutoff elect
Thank you, Justin !
I have add the output generated by grompp and mdrun at the end.
> Cun Zhang wrote:
> > hi, Justin. Thank you for your patience !
> >
> > I'm still in trouble with infinite CNT simulation.
> >
> > I'm trying to simulate the
have no repetitive rows
I upload a log file for more information in there (
http://4message.net/blog/wp-content/uploads/2009/11/CNT.tar.bz2 )
Cun Zhang wrote:
> > Hi, Justin.
> > Thank you for your help! I was intended to reply the third question
> > after I retryed the simulation u
Hi, Justin.
Thank you for your help! I was intended to reply the third question
after I retryed the simulation under your advice,but I haven't enough time
to do it. It's too late :)
Just now, I do a simulation. All seems ok. I will check it again.
Thank you again!
Cun Zhang
> &g
Justin, thanks for your reply. By the way, your GMX tutorials is great!
I post the gro file and mdp file at the end.
On Thu, Nov 19, 2009 at 10:09 PM, Justin A. Lemkul wrote:
>
> Not possible, Gromacs 4.1 hasn't been released :) If you're using version
> 4.0.1, you shouldn't, because it has a
Hi,gmx users,
I want to set CNT infinite
in the system of CNT and water. I'm using GMX 4.1,so I have set pbc=xyz,
periodic_molecules=yes in mdp file.
I set the box size larger than CNT's length a C-C bond(half up and half
down).
If I don't do a EM, it will crumble. But if I do it,it can't satisfy
Dear users,
I use the Cationic Dummy Atom methods by Pang to simulate a protein
containing Zn2+. How to get the parameters in [ virtual_sites? ] section? I use
the model 4fd.
In the following example, how to get the value of parameters a, b and d?
[ virtual sites4 ]
;
ou can increase fft grid spacing a little (just try several
values little larger)to lower PME mesh load to better distribute the
computation among nodes.
Regards,
Yinhe Zhang
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailm
pe= SI SI;
wall_density= 7.12 7.12 ; nm^{-2}, number density, 200 atom in
5.3x5.3nm^2
-
Regards,
Yinhe Zhang
On Wed, May 6, 2009 at 4:54 PM, Berk Hess wrote:
> Hi,
>
> I tried to reproduce this, but I did not succ
Dear all:
I extended a mdrun in GMX4.01,and the two trajectory files can not been
concatenated,i.e.the "trjcat"command is invalid in GMX4.01. How to solve this
question?
Thank you very much!
Sincerely
Zhang,Rui
ShanDong university___
You can use the mdrun command:
How to restart a crashed run. The mdrun program now uses a very handy
checkpointing feature.
Restarting crashed runs is easy with mdrun.
mdrun -s prev.tpr -f prev.trr -e prev.edr -o prev.trr –g prev.log –cpi -append
在2009-05-06，"Anna Marabotti" 写道：
>Dear al
s
E_x = 1 -0.55 0
Regards,
Yinhe Zhang
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Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un
The water box is about 10nm in z direction. x and y box sizes are about
3.3nm.
Hui
On Fri, Apr 24, 2009 at 7:17 PM, Mark Abraham wrote:
> Zhang Hui wrote:
>
>> Dear All,
>>
>> I just found that there is a problem when I extract the density
>> of wat
ingle precision.
Thanks for your help.
Hui Zhang
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don'
ingle precision.
Thanks for your help.
Hui Zhang
<>___
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Please search the archive at http://www.gromacs.org/search before posting!
Please don
Hi Mark,
I think 3.3.2, does it be fixed in 4.0?
Chao
On Wed, Feb 18, 2009 at 12:06 PM, Mark Abraham wrote:
> Chao Zhang wrote:
>
>> Dear gmx-user,
>>
>> I try to build a pure water box in Gromacs, so I just solved one water as
>> solute with genbox.
>>
&
lvent molecules to topology file (test.top)
--
Chao Zhang
___
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Please search the archive at
Hi, all,
Actually I think others have also noticed this "bug": g_energy often
generate incorrect heat capacity. When I checked the source code of
gmx_energy.c, I found the calculation of heat capacity is only related with
the fluctuation of temperature, which is actually the algorithm for NVE
Dear all:
Has anyone tried to run a NVE simulation for the coarse grained
dynamics using MARTINI force field? It's a little weird to me that 1fs/
step needs to be used to conserve the energy when protein is present
in the system. Does this make sense?
Thanks a lot.
Bin
--
;[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] How to calculate the local electric field?
> To: Discussion list for GROMACS users
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> Zhang Zhigang wrote:
> > Hi, all,
> &
Hi, all,
Is it possible to use an established program in Gromacs 4.0 package to
analysis the distributions of the local electric fields?
Let me explain the situation clearer as following:
In a pure water system, each molecule would "feel" a local electric
field (from the other molecu
Dear Angel,
Firstly I would quote a sentence of the manual: "Whether one needs to
correct for this contribution depends on what the PMF should represent."
Secondly, in my opinion, the so-called entropic contribution to the PMF
(we abbreviate it as P0) is a kind of reference PMF. That is to s
15:55:05 +0800
> From: "Zhang Zhigang" <[EMAIL PROTECTED]>
> Subject: [gmx-users] About entropic contribution to the potential of
>meanforce
> To: gmx-users@gromacs.org
> Message-ID:
><[EMAIL PROTECTED]>
> Content-Type: text/plain;
Hi,
In the manual of gromacs, the entropic contribution to the pmf is
emphasized. In my opinion, this contribution is originated from the
rotations of the constrained groups.
However, according to the manual suggestion, "...when calculating a PMF
between two solutes in a solvent, for the pu
?
Thanks in advance.
Bin
On Nov 24, 2008, at 1:32 AM, Xavier Periole wrote:
On Sun, 23 Nov 2008 21:48:52 -0800
BIN ZHANG <[EMAIL PROTECTED]> wrote:
Hi, all:
Has anyone done the coarse graining using MARTINI force field?
Could you give me any suggestion on how to build a
Hi, all:
Has anyone done the coarse graining using MARTINI force field?
Could you give me any suggestion on how to build a coarse grained
model from the AA system? I checked the website(http://md.chem.rug.nl/~marrink/MARTINI/Coordinates.html
) and it seems to me they only provide a scrip
Hi,
I'm using the newly published Gromacs 4.0 package these days. Compared
with the prior versions, this version seems to have been improved a
lot. From the ftp site, I've downloaded a manual for this version. But this
manual seems to be incompleted, which can be revealed in the descriptions of
Hi all,
I'm trying to use gromacs 4.0 to carried out some calculations with test
particle insertion algorithm.
Here are my operations:
0. Carried out a common NPT simulation with N molecules, I got the .trr
file;
1. prepare .top and .gro with N+1 molecules (including the test
particle);
Dear all
Thank you for browsing my question.When I run a K ion channel, I added DOPC
bilayer membrane, at the first mdrun, Gromacs program got Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains
Dear all
Thank you for browsing my question.When I run a K ion channel, I added DOPC
bilayer membrane, at the first mdrun, Gromacs program got Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains co
Dear all,
Is it possible to use GROMACS function(s) to calculate the averaged van der
Waals potential /Coulomb potential between a given residue and the rest
residues in the protein during a certain time of simulation?
Thanks,
LZhang
___
Hi to all,
I did surface calculation on a protein either with or without Cu-binding,
using g_sas with exactly the same parameter setting. For the delta solvation
energy from the output file (the the 5th column in the output file with a
label of D Gsol), non-Cu bound protein gives all 0, but
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