BIN ZHANG wrote:
Hi,:
Is it possible to solvate the system using coarse grained water
molecule?
I tried command: genbox -cp cg_protein.pdb -cs cgwat.pdb -o
cg_protein_water.pdb, but get Segmentation fault.
Can anyone give me some suggestion or basic procedure to build a
coarse
Hi,:
Is it possible to solvate the system using coarse grained water
molecule?
I tried command: genbox -cp cg_protein.pdb -cs cgwat.pdb -o
cg_protein_water.pdb, but get Segmentation fault.
Can anyone give me some suggestion or basic procedure to build a
coarse grained system?
Suman Chakrabarty wrote:
Dear all,
I have a very long trajectory split over a large number of files. What
would be the most efficient way to use the analysis programs over them?
Do they support multiple input for trajectory? Or I need to combine all
files into a single one anyway?
Use trjca
Suman Chakrabarty a écrit :
Dear all,
I have a very long trajectory split over a large number of files. What
would be the most efficient way to use the analysis programs over them?
Do they support multiple input for trajectory?
No most of the time, but you can easily analyze each part of your
Dear all,
I have a very long trajectory split over a large number of files. What
would be the most efficient way to use the analysis programs over them?
Do they support multiple input for trajectory? Or I need to combine all
files into a single one anyway?
Please help.
Regards,
Suman.
--
Thi
On Tue, Nov 25, 2008 at 1:40 AM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
>
>
> Suman Chakrabarty wrote:
>>
>> On Mon, Nov 24, 2008 at 11:46 PM, Justin A. Lemkul <[EMAIL PROTECTED]>
>> wrote:
Tcoupl = v-rescale
tc_grps = system
tau_t
Hi,
Indeed this bug has been fixed in 4.0.2.
Berk
> Date: Mon, 24 Nov 2008 11:00:46 -0500
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] problem in gromacs 4?
>
> Several users have reported this problem, i.e.:
>
> http://www.gromacs.org/pipermail/gmx-users/2
Suman Chakrabarty wrote:
On Mon, Nov 24, 2008 at 11:46 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
Tcoupl = v-rescale
tc_grps = system
tau_t= 0.1
ref_t= 300.00
Maybe you want "Protein Non-Protein" instead of "syste
On Mon, Nov 24, 2008 at 11:46 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
>> Tcoupl = v-rescale
>> tc_grps = system
>> tau_t= 0.1
>> ref_t= 300.00
>
> Maybe you want "Protein Non-Protein" instead of "system" here? But t
Hi everyone,
I'm having problems running an md simulation (with gmx-4.0.2) using vsites
and a time step of 4fs. I did generate the tpr with pdb2gmx. The problem
seems to occur when the molecule crosses pbc, since the first sign of the
simulation not working fine after ~3ns is
"
Warning: 1-4 int
[EMAIL PROTECTED] wrote:
Hi everyone,
I'm having problems running an md simulation (with gmx-4.0.2) using vsites
and a time step of 4fs. I did generate the tpr with pdb2gmx. The problem
seems to occur when the molecule crosses pbc, since the first sign of the
simulation not working fine after
Several users have reported this problem, i.e.:
http://www.gromacs.org/pipermail/gmx-users/2008-November/038181.html
Perhaps try upgrading to version 4.0.2 and try again.
-Justin
Bernhard Knapp wrote:
Dear users
I am trying to minimize the energy of a complex using gromacs 4. The
commands a
Dear users
I am trying to minimize the energy of a complex using gromacs 4. The
commands are the following:
pdb2gmx -f full_mCARKL_to_xylose_kinaseFH.pdb -o
full_mCARKL_to_xylose_kinaseFH.gro.pdb -p
full_mCARKL_to_xylose_kinaseFH.top -ignh
editconf -f full_mCARKL_to_xylose_kinaseFH.gro.pdb -
Waipot Ngamsaad wrote:
Hello Guys,
I am a newbie for GROMACS and MD also. I apologize if this is a stupid
question :).
Supposed I have a .gro file of 38 molecules of A which are already in
equilibrated conformations. Now I want to transform 15 molecules of A
into B therefore I will have t
Hello Guys,
I am a newbie for GROMACS and MD also. I apologize if this is a stupid question
:).
Supposed I have a .gro file of 38 molecules of A which are already in
equilibrated conformations. Now I want to transform 15 molecules of A into B
therefore I will have the binary mixture of A/B wit
Q. Y. HUAN wrote:
Dear Mark,
I am a bit confuse with yr advice,
after i did g_gyrate, I examine the gyration.xvg and I get this( I only show
part of the data):
@title "Radius of gyration"
@xaxis label "Time (ps)"
@yaxis label "Rg (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ l
Hello Ragnarok,
I am the author of acpypi and I believe Mark's guessing right. I strongly
suggest you to look my simple tutorial for some warnings about where to
place correctly the entries for amberff in *.top file:
http://code.google.com/p/acpypi/wiki/TutorialAcpypi4Gromacs
In particular: "*NB(
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 coarse grained model
from the AA system? I checked the
website(http://md.chem.rug.nl/~marri
minnu vijayan wrote:
hi all
i am a new user of gromacs. tried to run normal mode analysis. but
failed. i did up to mdrun.but in output i am not getting .mtx
file.(hesian matrix)
what may be the problem..can anybody help regarding this?
In order to attract the best possible response from the
hi all
i am a new user of gromacs. tried to run normal mode analysis. but failed. i
did up to mdrun.but in output i am not getting .mtx file.(hesian matrix)
what may be the problem..can anybody help regarding this?
On Fri, Nov 21, 2008 at 8:01 PM, Maria Musgaard <[EMAIL PROTECTED]> wrote:
> If yo
Dear Mark,
I am a bit confuse with yr advice,
after i did g_gyrate, I examine the gyration.xvg and I get this( I only show
part of the data):
@title "Radius of gyration"
@xaxis label "Time (ps)"
@yaxis label "Rg (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend bo
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