Hi All,
1. Artificial Shear Flow: I am trying to do translocation studies and wanted to
generate a shear flow without actual water atoms. I checked the mail list and
it was mentioned that there is no velocity profile but an option to accelerate
the atoms in a group. But I wanted to get the
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Mark Abraham [mark.abra...@anu.edu.au]
Sent: Tuesday, June 02, 2009 7:55 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] PME on BlueGene
Jakob Wohlert
Hi all users,
I am wondering how I can apply the shear force into the gromacs .Does anyone
has such experoence about that?
Really appreciate any suggestions.
Yang
___
gmx-users mailing listgmx-users@gromacs.org
Hi all users,
I just wonder how I can add the shear force in gromacs. I have checked the
manual but failed to find some effective ways to do that.
Any suggestions will be highly appreciated.
Thank you very much.
Yang
___
gmx-users mailing list
...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Mark Abraham [mark.abra...@anu.edu.au]
Sent: Monday, April 27, 2009 7:00 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] input the .gro and .trr file to the VMD
He, Yang wrote:
Hi all users,
I want to get some snap shots from
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of David van der Spoel [sp...@xray.bmc.uu.se]
Sent: Sunday, April 26, 2009 12:13 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] XTC.error
He, Yang wrote:
Hi all users,
When I run
-users-boun...@gromacs.org] On Behalf
Of Tsjerk Wassenaar [tsje...@gmail.com]
Sent: Tuesday, April 21, 2009 11:22 PM
To: jalem...@vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] about the bond connection between different groups
Hi He Yang, Justin,
You have said bonds between
thoroughly.
Cheers,
Tsjerk
On Wed, Apr 22, 2009 at 5:30 PM, He, Yang yang...@mavs.uta.edu wrote:
Hi Tsjerk,
Thank you for your reply. SO you mean I can just define the bond in one
moleculetype.As what you said, I have to renumber all atoms from one of the
moleculetypes,
starting at N+1
Hi all users,
I wonder whether it is allowed to define the bond connection between different
group in gromacs. Suppose atom A is in group1 and there is another atom B in
group2 .Then, I want to define bond between atom A and B. I am not sure whether
this is available in gromcas.
Thank you for
-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Tuesday, April 21, 2009 5:49 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] about the bond connection between different groups
He, Yang wrote:
Hi all users,
I wonder whether it is allowed
Hi all users,
I am trying to create the ndx file to define the atoms which I want to add the
position restraints to. What I create is like this:
[God]
21 22
[Bad]
61 62
And I have defined the atom numbering 21, 22, 61,62 in gro file like this :
2MOM bT 21 0.805 1.330
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Sunday, April 19, 2009 1:42 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] (no subject)
He, Yang wrote:
Hi all users,
I am trying to create the ndx file to define the atoms which I want to add
the position restraints to. What I create
.
Yang
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Sunday, April 19, 2009 3:47 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] (no subject)
He, Yang wrote:
Hi Justin
, April 19, 2009 3:47 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] (no subject)
He, Yang wrote:
Hi Justin,
In fact, I just get the error. I have tried to use the freezegroup but it
seems that it only work for the whole group not certain atoms in the whole
group.
Alright, so what's
, 2009 5:28 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] (no subject)
He, Yang wrote:
Hi Justin,
In fact, I have tried to use freezegrps to freeze a whole single CG DNA
strand and it works but if I want to freeze some atoms in this single
strand, it seems that I have no choice
HI all users,
I have tried a simple case with two atoms using [position_restraints] but
always it shows the same error :
Segmentation fault (core dumped)
But after I don't use the position_restraints for one atom and then I can run
the case smoothly. It seems that the gromacs doesn't
Hi all users,
I have used the position_restraints to restrict some atoms' activity but always
it shows that Segmentation fault (core dumped).
I can not fix this problem after trying many methods and hence, I just wonder
whether there are some other ways to restrict the atoms' movement in the
HI all users,
I want to define the position_restraints in the itp file but when I run it, it
always show that
Segmentation fault (core dumped)
and I will list the part below:
[position_restraints]
;ai funct fc
111 1 1
211 1 1
31
-users] the position_restraints
He, Yang wrote:
HI all users,
I want to define the position_restraints in the itp file but when I run it,
it always show that
Segmentation fault (core dumped)
You'll have to do better than run it - what do you mean, grompp? mdrun?
As written, your position
] the position_restraints
He, Yang wrote:
HI Justin,
I just use the mdrun command and then get such error. Before that, I did not
get other messages just go on well expect when I use the mdrun.
Also, when I did not use the position_restraints , it will run smoothly. As
long as I add this even though
Hi all users,
I need to add some dummy atoms in my case. I know that I need to include the
section [virtual_sites] in the top file but I am not sure how to define them in
the itp file .Do I need to list these atoms in the section[atoms] ? Can anyone
of you give me some suggestions about that?
Hi all users,
I need to define the hydrogen bonding interactions between bases in the CG DNA
model . Can anyone of you tell me how to do that in the gromacs force files?
Thank you very much in advance.
Yang
___
gmx-users mailing list
Hi all users,
When I try to input the .gro and .trr file into the VMD, I always find that
there is no bond connected among the atoms.But in fact, I have defined all the
bond connection in the gromacs files. Can anyone tell me how to get the snap
shots in the VMD with the bonds among the atoms?
Hi all users,
When I try to input the .gro and .trr file into the VMD, I always find that
there is no bond connected among the atoms.But in fact, I have defined all the
bond connection in the gromacs files. Can anyone tell me how to get the snap
shots in the VMD with the bonds among the atoms?
Hi all users,
When I try to input the .gro and .trr file into the VMD, I always find that
there is no bond connected among the atoms.But in fact, I have defined all the
bond connection in the gromacs files. Can anyone tell me how to get the snap
shots in the VMD with the bonds among the atoms?
/gmx-users/2009-February/039830.html
If you want free advice, take what you're given, demonstrate that you've made
some efforts to solve your problem, and follow up if you experience a *new*
issue.
-Justin
He, Yang wrote:
Hi all users,
When I try to input the .gro and .trr file into the VMD, I
Hi all users,
When I try to input the .gro and .trr file into the VMD, I always find that
there is no bond connected among the atoms.But in fact, I have defined all the
bond connection in the gromacs files. Can anyone tell me how to get the snap
shots in the VMD with the bonds among the atoms?
Hi all users,
When I try to input the .gro and .trr file into the VMD, I always find that
there is no bond connected among the atoms.But in fact, I have defined all the
bond connection in the gromacs files. Can anyone tell me how to get the snap
shots in the VMD with the bonds among the atoms?
-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Thursday, February 05, 2009 3:58 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] about the repelling of DNA base pair
He, Yang wrote:
Hi all users,
I am dealing
Hi all users,
I am dealing with the CG DNA model and I just list the parameters for non-bond
potential blow:
A T 10.00690.04109
P P 10.04352 4.352E-12
S S 10.04352 4.352E-12
A A 1
Hi all users,
I am wondering how to get the original pdb file for CG DNA model. I have looked
for this file in the website but no pdb file. Can anyone of you give me some
suggestions how to get such file ?
Thank you in advance.
Yang
___
gmx-users
Hi all users,
when I run the command grompp , it always shows that
processing coordinates...
Warning: atom names in DNA.top and DNA.gro don't match (N10 - N1)
Warning: atom names in DNA.top and DNA.gro don't match (Q11 - Q1)
Warning: atom names in DNA.top and DNA.gro don't match (Q12 - Q1)
Abraham [mark.abra...@anu.edu.au]
Sent: Tuesday, January 27, 2009 5:43 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the wanging: atom names don't match in top and gro
file
He, Yang wrote:
Hi all users,
when I run the command grompp , it always shows that
processing
Hi all the users,
When I use the command mdrunto simulate the CG DNA model, I found that all
the files are output expect the trajectory file. I will list some parts of my
mdp.file
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit
: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Friday, January 23, 2009 11:42 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] why the trajectory file is not output
He, Yang wrote:
Hi all the users,
When I
-users-boun...@gromacs.org] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Friday, January 23, 2009 11:55 AM
To: Gromacs Users' List
Subject: Re: [gmx-users] why the trajectory file is not output
He, Yang wrote:
I think this problem is not due to the disk space cause I check that it has
] On Behalf
Of Justin A. Lemkul [jalem...@vt.edu]
Sent: Friday, January 23, 2009 12:09 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] why the trajectory file is not output
He, Yang wrote:
yes, I mean that when using the command mdrun, the traj.xtc file is not
ouput at all while the other files
-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Mark Abraham [mark.abra...@anu.edu.au]
Sent: Friday, January 23, 2009 12:53 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] why the trajectory file is not output
He, Yang wrote:
I just tried it several times
Subject: Re: [gmx-users] course grain model for DNA
He, Yang wrote:
Hi all users,
when I am using the gromacs to simulate the course grain model for DNA, it
seems that the software doesn't recognize my force field file. I have
included all the bond and non-bond parameters in the bon.itp
impose distance
restraints on some of the hydrogen bonds at the ends. You need to
modify md.mdp to turn on distance restraints and have a new file
called disres.itp that mentions the distances to be restrained.
Hope this helps,
Mrinalini
On Wed, Nov 26, 2008 at 1:06 AM, He, Yang [EMAIL PROTECTED
Hi all users,
when I am using the gromacs to simulate the course grain model for DNA, it
seems that the software doesn't recognize my force field file. I have included
all the bond and non-bond parameters in the bon.itp and nb.itp file.
During my simulation , I found that the base pair for C-G
Hi all users,
I just use the gromacs to simulate the course grain model for DNA, but when I
run the simulation to see whether the two strands will separate under certain
temperature , I found that the disassociation will happen in the low
temperature . This is my part of mdp.file
;VARIOUS
in the mdp.file
Is it a real diassociation or an illusion? Visualize with PBC in mind.
To put them back, use trjconv to center one chain of the DNA and
output the two chains.
On 11/11/08, He, Yang [EMAIL PROTECTED] wrote:
Hi all users.
When I change the Temperature in the madp file to try to get
Hi all users,
When I change the temperature to try to get different disassociation about the
two DNA's strands. But even I change the value of temperature by 0K in the mdp
file ,
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl = berendsen
; Groups to
] On Behalf Of Justin A. Lemkul [EMAIL
PROTECTED]
Sent: Tuesday, November 11, 2008 12:12 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the temperature effect in the simulation
He, Yang wrote:
Hi all users,
When I change the temperature to try to get different disassociation
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the temperature effect in the simulation
He, Yang wrote:
Hi all users,
When I change the temperature to try to get different disassociation about
the two DNA's strands. But even I change the value of temperature by 0K in
the mdp file
Hi all users.
When I change the Temperature in the madp file to try to get different result
about DNA model's disassociation , but it is strange that result seems to be
the same for different Temperature. Even I change the Temperature by 0K ,the
disassociation happened.
I have tried to reduce
further suggestions,
Thank you .
Yang
From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Mark Abraham [EMAIL
PROTECTED]
Sent: Thursday, November 06, 2008 3:52 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] mdp file
He, Yang wrote:
Hi
Hi all users,
When I use the command mdrun -tablep table.xvg to run my model in gromacs,
it always shows that:
starting mdrun 'DNA in water'
1 steps, 20.0 ps.
Warning: 1-4 interaction between 11 and 19 at distance 1.437 which is larger
than the 1-4 table size 1.000 nm
These are
From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Justin A. Lemkul [EMAIL
PROTECTED]
Sent: Monday, November 03, 2008 4:22 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the mdp file
He, Yang wrote:
Hi all users,
When I change the value of nsteps in my mdp file to run
Hi all users,
When I change the value of nsteps in my mdp file to run the gromacs and show
the trajectory in the gromcas, I found that only the value of nsteps is set by
10, is there just the animation of the molecule's movement . I have tried many
time and set the other values of nsteps,
Hi all users,
I just encountered a problem about the DNA model when I set the coordinate in
the pdb file . It always shows very strange figure about the DNA model.
My pdb file is like this:
ATOM 1 Ab1 DNA 1 0.0510.575 0.516 1.0 0.0
ATOM 2 Tb1 DNA 1
Hi all users,
When I input the mdrun -table table_nonbond.xvg
it always shows that :
Fatal error:
Library file tablep.xvg not found in current dir nor in default directories.
(You can set the directories to search with the GMXLIB path variable)
Has anyone encountered the same problem? Can you
Hi all users,
I just use the command mdrun -table table_nonbond.xvg to run the table file
but it always shows that
Fatal error:
Tables in file table_nonbond.xvg not long enough for cut-off:
should be at least 1.90 nm
Actually, I have listed all the values up to 2.000nm in the file
Hi ,
I also encountered the same problem when I use the command:
mdrun -table table_nonbond.xvg
it shows that
Fatal error:
Library file bond_b0_b0.xvg not found in current dir nor in default
directories.
(You can set the directories to search with the GMXLIB path variable)
I wonder whether
-users] table command
He, Yang wrote:
Hi all users,
I just use the command mdrun -table table_nonbond.xvg to run the table file
but it always shows that
Fatal error:
Tables in file table_nonbond.xvg not long enough for cut-off:
should be at least 1.90 nm
Actually, I have listed
: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Mark Abraham [EMAIL
PROTECTED]
Sent: Saturday, October 25, 2008 10:37 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Fatal error: Invalid dihedral type 0
He, Yang wrote:
Hi Mark,
I have carefully adjusted the parameters
Hi all users,
I just use the grompp -f att.mdp -c atom_b4em.gro -p hust.top -maxwarn 10 -pp
and then always show the :
Fatal error:
Invalid dihedral type 0
and this is my bon.itp file;
[ bondtypes ]
; ij funcb0 kb
Ab SLa 1 0.6430 374468
Tb
From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Mark Abraham [EMAIL
PROTECTED]
Sent: Saturday, October 25, 2008 4:50 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Fatal error: Invalid dihedral type 0
He, Yang wrote:
Hi all users
-users] f(x) g(x) h(x)in the user defined potential functions
He, Yang wrote:
Hi all users,
When I am defining the user potential functions using the table, I
encountered a problem that there are several unstable parameters in the
separate f(x),g(x),h(x) .For example, in the g(x
To: gmx-users@gromacs.org
Subject: [gmx-users] how to use the new potential
He, Yang wrote:
Hi all users,
I am engaged in deal with the course grain model,in which the
potential functions are not the same as in gromacs.Hence, If I want to
use the new potentials , I guess I can change the source
Hi all users,
When I am defining the user potential functions using the table, I encountered
a problem that there are several unstable parameters in the separate
f(x),g(x),h(x) .For example, in the g(x), there is a parameter epsilon whose
value will depend on different pairs.In this
Hi all users,
I am engaged in deal with the course grain model,in which the potential
functions are not the same as in gromacs.Hence, If I want to use the new
potentials , I guess I can change the source code or use the table. But I never
have this experience about that.Can anyone of you give
Hi Jian,
Do you also need to change the source code to get a new potential function? I
am also engaged in this job. DO you have any experience about this job?
Regards,
Yang
From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Jian Zou [EMAIL
Hi all users,
I just got confused about whether I need to input the values of the coulombic
interaction in the nb.itp file .If not, I wonder how the gromacs will recognize
the coulombic interaction ,in the mdp.file?
Sorry for this dull question.
Thank you in advance.
Yang
Hi ,
I was also engaged in dealing with the problem about the course grain model . I
find that in this CG force field , the potential functions almost don't
correspond to that in the gromacs.
Hence, I wonder whether you know to how to define these new potential functions.
Thank you in
Hi all users,
Now I am using the gromacs to simulating the course model for DNA but I find
that the potential functions in this model are not found in the gromacs force
field . Can anyone tell me how to define these new potential functions in the
gromacs files?
The form fro the new
Hi all users,
When I use the editconf command to transform pdb file to gro file, it shows
like this
Opening library file /usr/share/gromacs/top/aminoacids.dat
Opening library file /usr/share/gromacs/top/atommass.dat
Opening library file /usr/share/gromacs/top/vdwradii.dat
Opening library file
.
Yang
From: [EMAIL PROTECTED] [EMAIL PROTECTED] On Behalf Of Justin A. Lemkul [EMAIL
PROTECTED]
Sent: Wednesday, October 15, 2008 4:36 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] transfer pdb to gro
He, Yang wrote:
Hi all users,
When I use the editconf command to transform pdb
Hi all users,
I juse encountered a problem when I run the code about the course grain for DNA,
it shows like this
creating statusfile for 1 node...
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...
calling cpp...
In file included from
PROTECTED]
Sent: Tuesday, October 14, 2008 12:01 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] gromacs
He, Yang wrote:
Hi all users,
I juse encountered a problem when I run the code about the course grain for
DNA,
it shows like this
creating statusfile for 1 node...
Back Off
Hi all,
I am using gromacs to simulate the course grain for DNA. it is called the
super-atoms including Phosphate (P),Sugar(S),Adenine base(Ab),Thymine(Tb). I
have defined them in the .atp file like this,
Ab 134.1; Adenine base
Tb 125.1; Thymine base
S 83.11; Sugar
P 94.97;
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