On 6/10/13 12:13 PM, Matt Bawn wrote:
I am beginning a simulation of my system following the lysozyme tutorial
but when I try to use genbox to solvate my system it asks me to provide the
coordinates of the center of the box. I have previously been successfully
able to enter the same commands wi
I am beginning a simulation of my system following the lysozyme tutorial
but when I try to use genbox to solvate my system it asks me to provide the
coordinates of the center of the box. I have previously been successfully
able to enter the same commands without this prompt appearing from gromacs.
On 4/29/13 5:30 AM, Alexander Björling wrote:
Dear users,
I am trying to solvate a MARTINI model, using a pre-equilibrated
coarse-grained water box. This usually works fine with the following
command.
genbox -cs water-1bar-303K.gro -cp 01min.gro -o 02solv -vdwd 0.21
When I recently increased
genbox works best when the box size of the solute is defined as the same as of
the water one used to solvate it. So you can build a water box with the
dimensions you want and them use it.
You can build a water box by using genconf -nbox and use a script to cut to the
dimensions you need, mini
Dear users,
I am trying to solvate a MARTINI model, using a pre-equilibrated
coarse-grained water box. This usually works fine with the following
command.
genbox -cs water-1bar-303K.gro -cp 01min.gro -o 02solv -vdwd 0.21
When I recently increased the box size things started going wrong. As the
s
On 1/13/13 11:00 AM, Kieu Thu Nguyen wrote:
Dear All,
When i use the command
genbox -ci single.gro -nmol 175 -box 7.5 7.5 7.5 -try 100 -o 175_noW.gro
the error is
Segmentation fault (core dumped)
What does it mean ?
Google can tell you all about segmentation faults. You probably ran out
On 1/2/13 4:20 AM, Mijiddorj wrote:
I am a new user of Gromacs, I have problem with genbox. When I run genbox
following error occurred:Program genbox, VERSION 4.5.5Source code file:
/build/buildd/gromacs-4.5.5/src/gmxlib/futil.c, line: 491File input/output
error:/home/mijiddorj/Desktop/Tutorial
I am a new user of Gromacs, I have problem with genbox. When I run genbox
following error occurred:Program genbox, VERSION 4.5.5Source code file:
/build/buildd/gromacs-4.5.5/src/gmxlib/futil.c, line: 491File input/output
error:/home/mijiddorj/Desktop/Tutorial02/1AKI1.topFor more information and
tip
Thank you very much. I got it sorted out by following your advice.
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Dec 31, 2012, at 10:23 PM, Justin Lemkul wrote:
>
>
> On 12/31/12 9:41 PM, Xu Dong Huang wrote:
>> Dear Advanced Gr
On 12/31/12 9:41 PM, Xu Dong Huang wrote:
Dear Advanced Gromacs users,
I'm trying to generate a solvated system with >1 solute (In my case 3). I do
genbox -cp polymer.gro -nmol 2 -ci polymer.gro -cs water.gro -o polymer_solv.gro
-p polymer.top
My polymer molecule contains 201 atoms. box siz
Dear Advanced Gromacs users,
I'm trying to generate a solvated system with >1 solute (In my case 3). I do
genbox -cp polymer.gro -nmol 2 -ci polymer.gro -cs water.gro -o
polymer_solv.gro -p polymer.top
My polymer molecule contains 201 atoms. box size 45x45x45
and it generates a system with th
So perhaps you don't need a box this big?
a box length of 25 nm might be within your available memory. Otherwise, talk to
your cluster's sysadmins.
I am not sure that you're going to get any useful statistics on a box of length
250 nm in any event. A box that size will fit about 1 billion atoms
Thanks..You are right...The last line of gro file says 250 so it is in nm!...
On 10 October 2012 12:30, Christopher Neale
wrote:
> Sounds like you ran out of memory. Many clusters have a few large-memory
> nodes. Can you use one of those?
> It's failing on a call for 1.3 Gb of memory, which by i
Sounds like you ran out of memory. Many clusters have a few large-memory nodes.
Can you use one of those?
It's failing on a call for 1.3 Gb of memory, which by itself isn't really a
lot...
Also, can you confirm 250 A box length, not 250 nm box length? Gromacs defines
length in units of nm.
Chr
Gavin Melaugh wrote:
Hi all
I have a system of 40 solute molecules in a solvent of 480 crown ether
molecules. I am not trying to insert 100 methane molecules into this
relaxed and well equilibrated structure using genbox.
There are clearly visible cavities in the fluid but genbox only alllows
Hi all
I have a system of 40 solute molecules in a solvent of 480 crown ether
molecules. I am not trying to insert 100 methane molecules into this
relaxed and well equilibrated structure using genbox.
There are clearly visible cavities in the fluid but genbox only alllows
the insertion of 8 methan
saly jackson wrote:
Hi all
Would you please let m eknow f we use 'genconf' after that we must use
'genbox' before applying 'grompp'?
It depends entirely upon what you want to do. I could think of a dozen ways to
combine both tools, in different orders, to achieve completely different ta
Hi all
Would you please let m eknow f we use 'genconf' after that we must use
'genbox' before applying 'grompp'?
Thanks
Regards
Saly
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Dear Gmx Users,
I am preparing my protein-ligand complex system for Umbrella Sampling (free
binding energy of ligand) and I set
up the box (Pulling with Z coordinate):
editconf -f Protein10LIGrot.pdb -o ProteinLIGbox.pdb -box 12 7 13
Then using VMD I placed my Protein-Lig complex to on the r
You can use the command genbox -cs with the option -maxsol number to
specify the number of water molecules
Good luck
Cuong
2012/1/16 vidhya sankar
> Hello Justin,
> Thanks for your patient reply
>
> I would like to solvate my molecules with specific
> number
On 16/01/12, vidhya sankar wrote:
>
>
>
>
>
>
>
>
>
>
>
>
>
> Hello Justin,
>
> Thanks for your patient reply
>
>
> I would like to solvate my molecules with specific number
> of water molecules
> what option is a su
Hello Justin,
Thanks for your patient reply
I would like to solvate my molecules with specific number of
water molecules
what option is a suitable to do that ? in editconf
with regards
S.Vidhya sankar
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shivangi nangia wrote:
Hi All,
I have a question about genbox -shell option.
The online manual says:
*-shell*real0 thickness of optional water layer around solute
The value specified for -shell option, example 3, produces a sphere with
radius 3 nm or diameter 3 nm?
Hi All,
I have a question about genbox -shell option.
The online manual says:
*-shell* real 0 thickness of optional water layer around solute
The value specified for -shell option, example 3, produces a sphere with
radius 3 nm or diameter 3 nm?
Thanks,
SN
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gmx-users mailing listgmx-us
Justin A. Lemkul wrote:
Fabian Casteblanco wrote:
Hello,
I was wondering if someone can help me with a general genbox question.
I have been using the command line:
genbox -ci octanol.gro -nmol 1000 -box 5 5 5 -o prop_1000.gro
to fill a box with 1000 molecules of octanol. With the smalle
Fabian Casteblanco wrote:
Hello,
I was wondering if someone can help me with a general genbox question.
I have been using the command line:
genbox -ci octanol.gro -nmol 1000 -box 5 5 5 -o prop_1000.gro
to fill a box with 1000 molecules of octanol. With the smaller
n-alcohols, it worked fin
Hello,
I was wondering if someone can help me with a general genbox question.
I have been using the command line:
genbox -ci octanol.gro -nmol 1000 -box 5 5 5 -o prop_1000.gro
to fill a box with 1000 molecules of octanol. With the smaller
n-alcohols, it worked fine but as I started using 1-but
Alright, thanks.
Majid
From: Justin A. Lemkul
To: Gromacs Users' List
Sent: Sun, April 17, 2011 12:31:49 PM
Subject: Re: [gmx-users] genbox output taking forever to complete
majid hasan wrote:
> Okay, so here is an output attached, for cubic box o
Okay, thank you.
Majid
From: Justin A. Lemkul
To: Gromacs Users' List
Sent: Sun, April 17, 2011 12:28:47 PM
Subject: Re: [gmx-users] genbox output taking forever to complete
majid hasan wrote:
> Okay, so here is an output attached, for cubic box o
majid hasan wrote:
Okay, so here is an output attached, for cubic box of length 10 (I
removed some atoms to reduce the size below 50kB).
Please do not attach coordinate files unless requested. Most people who are
uninterested in this thread do not want to waste time downloading large emai
majid hasan wrote:
Okay, so here is an output attached, for cubic box of length 10.
Actually, the carbon atoms are all placed at 00
Then your box size is overkill. All you're going to end up doing is adding tens
of thousands of waters that do not serve any purpose for most applications.
Okay, so here is an output attached, for cubic box of length 10 (I removed some
atoms to reduce the size below 50kB).
Actually, the carbon atoms are all placed at 0
To: Gromacs Users' List
Sent: Sun, April 17, 2011 4:39:56 AM
Subject: Re: [gmx-users] genbox output taking forev
:39 PM
*Subject:* Re: [gmx-users] genbox output taking forever to complete
Justin A. Lemkul wrote:
>
>
> majid hasan wrote:
>> Dear All,
>>
>> I am trying to add a single strand dna, and single walled carbon
nanotube in a box using the genbox command. Afte
tance between molecules inside the box,
and how can I make sure that they are placed at a reasonable distance inside
the
solvent?
Thanks,
Majid
From: Justin A. Lemkul
To: Gromacs Users' List
Sent: Sat, April 16, 2011 6:19:39 PM
Subject: Re: [gmx-use
Okay, thanks Justin!.
Majid
From: Justin A. Lemkul
To: Gromacs Users' List
Sent: Sat, April 16, 2011 6:19:39 PM
Subject: Re: [gmx-users] genbox output taking forever to complete
Justin A. Lemkul wrote:
>
>
> majid hasan wrote:
>> D
Justin A. Lemkul wrote:
majid hasan wrote:
Dear All,
I am trying to add a single strand dna, and single walled carbon
nanotube in a box using the genbox command. After typing following
command:
genbox -cp cntcapped.pdb -cs spc216.gro -ci ssgcg.gro -nmol 1 -box 2 2
2 -o cntdna.gro,
I
majid hasan wrote:
Dear All,
I am trying to add a single strand dna, and single walled carbon
nanotube in a box using the genbox command. After typing following command:
genbox -cp cntcapped.pdb -cs spc216.gro -ci ssgcg.gro -nmol 1 -box 2 2 2
-o cntdna.gro,
I get: Reading solute configur
Dear All,
I am trying to add a single strand dna, and single walled carbon nanotube in a
box using the genbox command. After typing following command:
genbox -cp cntcapped.pdb -cs spc216.gro -ci ssgcg.gro -nmol 1 -box 2 2 2 -o
cntdna.gro,
I get: Reading solute configuration
Containing 168
Fabian Casteblanco wrote:
Hello,
I'm trying to place 1000 molecules of 1-propanol using CHARMM FF
parameters in a -box 6 6 6. After minimization, I realized that for
a single molecule, the potential was slightly above 0, '+24 kJ/mol' to
be exact, with electrostatic coloumb potential the grea
Hello,
I'm trying to place 1000 molecules of 1-propanol using CHARMM FF
parameters in a -box 6 6 6. After minimization, I realized that for
a single molecule, the potential was slightly above 0, '+24 kJ/mol' to
be exact, with electrostatic coloumb potential the greatest
contributor. I used the
leila separdar wrote:
I have .gro and .top of a nanoparticle at temperature 1K and I want to
add the simulation box some other atomes at temperature 300K. is there
any body knows how can I do it. I have used (genbox -cp
nanoparticle.gro -ci otheratom.gro -p nanoparticle.top -o out) but it
add
I have .gro and .top of a nanoparticle at temperature 1K and I want to
add the simulation box some other atomes at temperature 300K. is there
any body knows how can I do it. I have used (genbox -cp
nanoparticle.gro -ci otheratom.gro -p nanoparticle.top -o out) but it
add more than atomes than I ex
Hi,
I am getting following output after using editconf to create a box
followed by
genbox_d_mpi -cp be.gro -p topol.top -ci be.gro -nmol 2 -o out.gro
This time i tried to insert just 2 molecules still the command is not
working.
---
Opening library file
/global
On 12/02/2011 12:51 PM, Rini Gupta wrote:
Hello Mark,
Thanks for the reply.
I tried to first make a box using editconf
editconf_d_mpi -f conf.gro -o be.gro -bt cubic -box 2.7 2.7 2.7
Box is successfully created and then I use
genbox_d_mpi -cp be.gro -p topol.top -ci be.gro -nmol 19 -o out.gr
Hello Mark,
Thanks for the reply.
I tried to first make a box using editconf
editconf_d_mpi -f conf.gro -o be.gro -bt cubic -box 2.7 2.7 2.7
Box is successfully created and then I use
genbox_d_mpi -cp be.gro -p topol.top -ci be.gro -nmol 19 -o out.gro
still, I am getting only one B
On 12/02/2011 12:22 PM, Justin A. Lemkul wrote:
Do the -ci and -cs steps separately and see if that gives you the
proper output. I have found that the two are incompatible, but in
theory, I don't know why one couldn't do everything in one step.
It can depend on the assumptions about the purp
On 12/02/2011 7:51 AM, Rini Gupta wrote:
Dear gmx users,
I am using gromacs (version 4.0.7)
to setup a 2-butoxyethanol-water simulation.
I created topology and coordinate file (.pdb) for BE using AUTOMATED
TOPOLOGY BUILDER server.
It created a topology file (for united atom) compatible with GRO
Rini Gupta wrote:
Dear gmx users,
I am using gromacs (version 4.0.7)
to setup a 2-butoxyethanol-water simulation.
I created topology and coordinate file (.pdb) for BE using AUTOMATED
TOPOLOGY BUILDER server.
It created a topology file (for united atom) compatible with GROMOS
ffG53a6 forcefie
Dear gmx users,
I am using gromacs (version 4.0.7)
to setup a 2-butoxyethanol-water simulation.
I created topology and coordinate file (.pdb) for BE using AUTOMATED TOPOLOGY
BUILDER server.
It created a topology file (for united atom) compatible with GROMOS ffG53a6
forcefield.
I want to generat
On 6/11/2010 12:54 AM, Diana Lousa wrote:
Dear all,
I tried to send this message earlier, but I had attached a pdb file
and apparently it exceeded the size allowed in the mailing list and is
awinting for the list moderator to evaluate it. I apologize if the
message is sent twice.
I am trying
Diana Lousa wrote:
Dear all,
I tried to send this message earlier, but I had attached a pdb file and
apparently it exceeded the size allowed in the mailing list and is
awinting for the list moderator to evaluate it. I apologize if the
message is sent twice.
I am trying to solvate a protei
Dear all,
I tried to send this message earlier, but I had attached a pdb file and
apparently it exceeded the size allowed in the mailing list and is awinting
for the list moderator to evaluate it. I apologize if the message is sent
twice.
I am trying to solvate a protein in a box of acetonitrile u
Dear users,
When I'm trying to create my solve box of 12x12x12 nm I encounter some trouble.
I'm using Gromacs 4.5 with the MARTINI force field to set up a system of 400
dipeptide molecules in water. However when I use "genbox -cp -cs -vdwd 0.2 -o " I get an
inhomogeneous distribution of the w
Pim Frederix wrote:
Dear users,
I'm trying to create a box with a number (64) of small peptide molecules
(diphenylalanine) solved in ethanol for a Gromacs run with the Martini
coarse-grain force field. I've created the box with the solute with the
genbox -ci command: genbox -ci FFMM_cg.pdb -nm
Dear users,
I'm trying to create a box with a number (64) of small peptide molecules
(diphenylalanine) solved in ethanol for a Gromacs run with the Martini
coarse-grain force field.
I've created the box with the solute with the genbox -ci command: genbox -ci
FFMM_cg.pdb -nmol 64 -box 5 5 5 -o F
Tandia, Adama wrote:
Dears,
I'm generating a box filled with NO3 molecules using Gromacs 3.3:
Any particular reason you're using software that is five years old? Unless
you've got a particular reason (i.e. continuity with older work), I'd strongly
recommend upgrading to version 4.0.7 for
Dears,
I'm generating a box filled with NO3 molecules using Gromacs 3.3:
genbox -ci molecule.gro -p molecule.top -o bigbox.gro -box 4.0 4.0 4.0
-nmol 800 -vdwd 0.2
The file bigbox.gro is generated but molecules are entangled. This makes
the geometry optimization to remove close contact impossib
Sai Pooja wrote:
Hi,
I am using CHARMM forcefield with the tip3p. What input file(-cs) should
i use to solvate the protein using the genbox command? The default is
spc216.gro. What would be compatible with my system?
I looked up the directory which has spc216.gro file. It has tip4p.gro
fi
Hi,
I am using CHARMM forcefield with the tip3p. What input file(-cs) should i
use to solvate the protein using the genbox command? The default is
spc216.gro. What would be compatible with my system?
I looked up the directory which has spc216.gro file. It has tip4p.gro file
but for some reason do
will simply replicate the unit.
>>
>>
> That works. Glad you found a solution.
>
> -Justin
>
> Fahimeh
>>
>> > Date: Tue, 20 Apr 2010 09:12:44 -0400
>> > From: jalem...@vt.edu
>> > To: gmx-users@gromacs.org
>> > Subject: Re: [g
a solution.
-Justin
Fahimeh
> Date: Tue, 20 Apr 2010 09:12:44 -0400
> From: jalem...@vt.edu <mailto:jalem...@vt.edu>
> To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
> Subject: Re: [gmx-users] genbox
>
44 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] genbox
>
>
>
> fahimeh bafti wrote:
> > Thank you Justin
> > but I end up with a new error. now in the insert.pdp file I have a
> > molecule which I need to add 4 c
icate the unit.
Fahimeh
> Date: Tue, 20 Apr 2010 09:12:44 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] genbox
>
>
>
> fahimeh bafti wrote:
> > Thank you Justin
> > but I end up with a new error. now in the insert.pdp fi
sidue (i.e.,
through renaming and renumbering) and then convert it back, but that sounds like
a mess. Probably #2 is the easiest.
-Justin
Fahimeh
> Date: Tue, 20 Apr 2010 07:10:59 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] genbox
&g
Fahimeh
> Date: Tue, 20 Apr 2010 07:10:59 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] genbox
>
>
>
> fahimeh bafti
> > Hello,
> >
> > I want to use a file.pdb which has 8 chain of polypeptide, each chain
> >
fahimeh bafti wrote:
Hello,
I want to use a file.pdb which has 8 chain of polypeptide, each chain
contains 6 residues. I need to expand it to 12 chains of 6 rsidues so I
need to add 4 chains or in the other word 24 residues. I think I have to
use genbox, so I make another copy of file.pdb
Hello,
I want to use a file.pdb which has 8 chain of polypeptide, each chain contains
6 residues. I need to expand it to 12 chains of 6 rsidues so I need to add 4
chains or in the other word 24 residues. I think I have to use genbox, so I
make another copy of file.pdb and rename it to insert.
On 28/01/10 13:06, Lum Nforbi wrote:
Hello all,
Can someone tell me the meaning of this error message after using the
genbox command?
Certainly not without more useful information - GROMACS version,
simulation system size, actual command line. Even then, the best guess
is probably that you'r
Hello all,
Can someone tell me the meaning of this error message after using the genbox
command?
*** glibc detected *** genbox: munmap_chunk(): invalid pointer: 0x095969c8
***
=== Backtrace: =
/lib/tls/i686/cmov/libc.so.6[0xb7e7c454]
genbox[0x81195c4]
=== Memory map:
0804
Lum Nforbi wrote:
Hello all,
How long does it usually take genbox to run?
Generally, a few seconds, but that will depend on the size of your system and
what you're trying to do (simple solvation, molecule insertion, etc). It is not
possible to say for certain, since processor speed an
Hello all,
How long does it usually take genbox to run?
Thanks,
Lum
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iulek wrote:
Thanks for replying.
Humm..., maybe I see now. As a beginner I intended to keep all files
produced and better inspect what happens in sequence, but I did not want
to use the conventional renaming. But it seems that for the topology
file, the common procedure is to keep al
Thanks for replying.
Humm..., maybe I see now. As a beginner I intended to keep all files
produced and better inspect what happens in sequence, but I did not want
to use the conventional renaming. But it seems that for the topology
file, the common procedure is to keep always one only na
iulek wrote:
Hi!
I am a very beginner, trying to make some dynamics of a protein in a
water box, after doing some (web) tutorials. I googled first for this
(possibly simple) error, found one reference, but cannot see it,
possibly because the gromacs site is under changes.
I ran pdb
Hi!
I am a very beginner, trying to make some dynamics of a protein in
a water box, after doing some (web) tutorials. I googled first for this
(possibly simple) error, found one reference, but cannot see it,
possibly because the gromacs site is under changes.
I ran pdb2gmx and editconf
On Thu, Feb 19, 2009 at 01:56:28AM +1100, Mark Abraham wrote:
> Chao Zhang wrote:
> >Hi Mark,
> >
> >I think 3.3.2, does it be fixed in 4.0?
>
> I don't know - I've not seen it reported. You should search the mailing
> list archives.
I've solvated with tip4p in 3.3cvs and 3.3.1, never had the pr
Chao Zhang wrote:
Hi Mark,
I think 3.3.2, does it be fixed in 4.0?
I don't know - I've not seen it reported. You should search the mailing
list archives.
There won't be any interest in diagnosing or fixing it within version
3.x, but if you can reproduce your result in 4.0.4, file a bugzill
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.
>>
>> When I use tip3p water, my scripts wor
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.
When I use tip3p water, my scripts work well. But to switch to tip4p
water, there seems a bug, I don't know whether people have noticed this
or not.
The system sh
Dear gmx-user,
I try to build a pure water box in Gromacs, so I just solved one water as
solute with genbox.
When I use tip3p water, my scripts work well. But to switch to tip4p water,
there seems a bug, I don't know whether people have noticed this or not.
The system shows that it added 350 wat
Sunil Thapa wrote:
Respectable Mark
I am studying diffusion of oxygen in water. Can I specify the number of
water molecules for a particular size of box. For example, I need to
have 98 water molecules and 2 oxygen molecules in one solution. After
that I need to increase the number of oxygen mo
Respectable Mark
I am studying diffusion of oxygen in water. Can I specify the number of water
molecules for a particular size of box. For example, I need to have 98 water
molecules and 2 oxygen molecules in one solution. After that I need to increase
the number of oxygen molecules and decrease
Chih-Ying Lin wrote:
Hi
Originally, in the topol.top file =>
[molecule]
solute 1
After the command:
genbox -cp one_solute.gro -cs spc216.gro -ci one_solute.gro -nmol N
-p topol.top
in the topol.top file =>
[molecule]
solute 1
solvent 5000
I think the flag "-p topol.top" in the genb
Hi
Originally, in the topol.top file =>
[molecule]
solute 1
After the command:
genbox -cp one_solute.gro -cs spc216.gro -ci one_solute.gro -nmol N -p
topol.top
in the topol.top file =>
[molecule]
solute 1
solvent 5000
I think the flag "-p topol.top" in the genbox command did not do it
corr
Hi,
there seems to be a problem when using genbox with triclinic boxes as
solvent input. I have a frame 0.pdb from an equilibrated MD simulation
of a triclinic box. When I take the water from the box as solvent input
and the protein as "protein input" for genbox:
echo SOL | editconf -ndef -f
Hello,
I have a problem about genbox command in GMX. I'm running genbox to randamly
insert molecules. Because the probobility of successful insertion is low, I
have to use a large number for the "-try" variable. After running genbox I
found sometimes the memory cost increased gradually after ea
JW Feng wrote:
David,
The results from using version 3.3.1 is different from version 3.3.2.
In version 3.3.1, adding "SOL OL 0" and executing "genbox -cs
tip5p.gro -box 1 1 1" created a box with 37 SOL molecules but the
density is too high at 3072.87 g/L.
In version 3.3.2, adding "SOL OL 0" di
David,
The results from using version 3.3.1 is different from version 3.3.2.
In version 3.3.1, adding "SOL OL 0" and executing "genbox -cs
tip5p.gro -box 1 1 1" created a box with 37 SOL molecules but the
density is too high at 3072.87 g/L.
In version 3.3.2, adding "SOL OL 0" did not work. Howe
JW Feng wrote:
Hello,
I used genbox (version 3.3.1 and 3.3.2) to create a 1nm box of SPC,
TIP4P and TIP5P water with "
genbox -cs .gro -box 1 1 1". The TIP5P box contains half
the number of water molecules compared to TIP4P and SPC.
SPC: 33 SOL molecules, density=987.205 (g/l)
TIP4P: 31 SOL
Hello,
I used genbox (version 3.3.1 and 3.3.2) to create a 1nm box of SPC,
TIP4P and TIP5P water with "
genbox -cs .gro -box 1 1 1". The TIP5P box contains half
the number of water molecules compared to TIP4P and SPC.
SPC: 33 SOL molecules, density=987.205 (g/l)
TIP4P: 31 SOL molecules
TIP5P:
Hi,
I am wanting to solvate a protein w/o adding H2O to its interior.
Reasons:
1. I am interested to know how the structural H2Os behave initially
w/o interference from added H2O.
2. Added H2O also introduce steric constraints that prevent EM from
achieving its goal, even w/o constrain
Alif M Latif wrote:
Dear GROMACS users and developers..
I'm trying to run MD simulation on a micelle structure, which i've built
using Packmol. The problem is when i use genbox to solvate the system
using SPC water, the water came inside the micelle, and my simulation
didn't produce any sign
If you have the center coordinates and your cell has a good radial symmetry, i
would just write a script, checking the distance of each water to the center
and then skipping everything below the radius of your cell.
Cheers
Martin
___
gmx-users
> Dear GROMACS users and developers..
>
> I'm trying to run MD simulation on a micelle structure, which i've built
> using Packmol. The problem is when i use genbox to solvate the system
> using SPC water, the water came inside the micelle, and my simulation
> didn't produce any significant changes
Dear GROMACS users and developers..
I'm trying to run MD simulation on a micelle structure, which i've built using
Packmol. The problem is when i use genbox to solvate the system using SPC
water, the water came inside the micelle, and my simulation didn't produce any
significant changes to the
esday, May 29, 2007 6:35 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Genbox problem ...
Kedar Potdar wrote:
> Hi friends,
>
>
>
> I have compiled Gromacs on native windows. The first two program in demo
> script (perl implementation of script "dem
Kedar Potdar wrote:
Hi friends,
I have compiled Gromacs on native windows. The first two program in demo
script (perl implementation of script “demo”) work fine but genbox
displays following output
Reading solute configuration
Glycine aRginine prOline Methionine Alanine Cystine Serin
Hi friends,
I have compiled Gromacs on native windows. The first two program in demo
script (perl implementation of script "demo") work fine but genbox displays
following output
Reading solute configuration
Glycine aRginine prOline Methionine Alanine Cystine Serine
Containing 145 atoms i
From: "Mark Abraham" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: "Discussion list for GROMACS users"
Subject: Re: [gmx-users] genbox give coord file more waters than top file
Date: Thu, 8 Mar 2007 22:27:01 +1100 (EST)
> 8 mar 2007
> 8 mar 2007 kl. 01.32 skrev Mark Abraham:
>
>>> Dear gromacs guys
>>>
>>> Why would genbox put more water molecules in my .gro file than in
>>> my .top
>>> file? I'm sure all I have to do is edit the number in my top file,
>>> but I
>>> have not had this happen before, does anyone know of a reaso
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