date:20091013

I jumped to the conclusion too fast. Thanks Justin for correcting me.
Disregard my previous comment please.

On Tue, Oct 13, 2009 at 10:35 PM, Justin A. Lemkul  wrote:

>
>
> Yongchul Chung wrote:
>
>> I think your box is too small. try changing them.
>>
>>
> What leads you to this conclusion?  We have no information about the box.
> Presumably, the only box that is "too small" would be one that doesn't
> satisfy the minimum image convention, but grompp fails with a fatal error in
> that case.
>
> -Justin
>
>  On Tue, Oct 13, 2009 at 8:05 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Nilesh Dhumal wrote:
>>
>>Hello,
>>
>>I am trying to equilibrate glucose in water using Gromacs
>>4.0.5 version.  I am geting the error immidiately after the
>>mdrun starts
>>Warning: 1-4 interaction between 1 and 18 at distance 3.462 which
>> is
>>larger than the 1-4 table size 2.400 nm
>>These are ignored for the rest of the simulation
>>This usually means your system is exploding,
>>if not, you should increase table-extension in your mdp file
>>or with user tables increase the table size
>>p0_4238:  p4_error: interrupt SIGSEGV: 11
>>Killed by signal 2.
>>
>>
>>Have you searched the website?  You would have undoubtedly found this:
>>
>>
>>
>> http://www.gromacs.org/Documentation/Errors#1-4_interaction_not_within_cut-off
>>
>>You should also search the list archive.  This problem shows up
>>weekly, if not daily sometimes.
>>
>>
>>Is the problem in mdp file?
>>
>>
>>Nothing seems obviously wrong.
>>
>>-Justin
>>
>>
>>Nilesh
>>
>>Here is my pr.mdp file
>>title   =  cpeptid position restraining
>>cpp =  /usr/bin/cpp
>>constraints =  none
>>integrator  =  md
>>dt  =  0.002; ps !
>>nsteps  =  20  ; total 1.0 ps.
>>nstcomm =  1
>>nstxout =  10
>>nstvout =  1000
>>nstfout =  0
>>nstlog  =  10
>>nstenergy   =  10
>>nstlist =  10
>>ns_type =  grid
>>rlist   =  1.0
>>coulombtype = PME
>>vdwtype = cut-off
>>rcoulomb=  1.0
>>rvdw=  1.4
>>fourierspacing  = 0.12
>>fourier_nx   = 0
>>fourier_ny   = 0
>>fourier_nz   = 0
>>pme_order   = 4
>>ewald_rtol  = 1e-5
>>optimize_fft= yes
>>; Berendsen temperature coupling is on
>>Tcoupl = Berendsen
>>tau_t = 0.1
>>tc-grps  =system
>>ref_t =   350
>>; Pressure coupling is  on
>>Pcoupl  = Berendsen
>>pcoupltype  = isotropic
>>tau_p   =  0.5
>>compressibility =  4.5e-5
>>ref_p   =  1.0
>>; Generate velocites is on at 300 K.
>>gen_vel =  yes
>>gen_temp=  350.0
>>gen_seed=  173529
>>
>>
>>
>>
>>
>>
>>
>>___
>>gmx-users mailing listgmx-users@gromacs.org
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search
>>before posting!
>>Please don't post (un)subscribe requests to the list. Use the
>>www interface or send it to gmx-users-requ...@gromacs.org
>>.
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>--
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu  | (540) 231-9080
>>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
>>
>>___
>>gmx-users mailing listgmx-users@gromacs.org
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search before
>>posting!
>>Please don't post (un)subscribe requests to the list. Use the www
>>interface or send it to gmx-users-requ...@gromacs.org
>>.
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>>
>> --
>> Yongchul "Greg" Chung
>> Graduate Student
>> Dept. of Chemical Engineering, Case Western Reserve University
>>
>
> --
> 
>
>

RE: [gmx-users] interpolation for tabulated potential

2009-10-13 Thread LuLanyuan

I saw it. Thanks.
Lanyuan

> Date: Wed, 14 Oct 2009 14:50:02 +1100
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] interpolation for tabulated potential
> 
> LuLanyuan wrote:
> > Hello,
> > I'm just wondering what interpolation method is used for the tabulated 
> > potential function in GMX. Since GMX 4, the input table contains 
> > potential and force, unlike potential and second derivative in GMX 3. Is 
> > cubic spline still used in GMX 4? If yes, what algorithm is implemented 
> > to get second derivative needed for cubic spline?
> 
> That's all in the manual. Please start there.
> 
> Mark
> ___
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Re: [gmx-users] interpolation for tabulated potential

LuLanyuan wrote:
> Hello,
> I'm just wondering what interpolation method is used for the tabulated 
> potential function in GMX. Since GMX 4, the input table contains 
> potential and force, unlike potential and second derivative in GMX 3. Is 
> cubic spline still used in GMX 4? If yes, what algorithm is implemented 
> to get second derivative needed for cubic spline?

That's all in the manual. Please start there.

Mark
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Re: [gmx-users] run g_cover in parallel

Itamar Kass wrote:

Hi,

This is strange, 'cause on the site under installing (using MPI) it is 
written "/In GROMACS 4.x, some of the utility programs are also 
MPI-aware, but these will only be for compute-intensive utilities (e.g. 
that diagonalize large matrices, or calculate autocorrelations, etc.)./".

So I guess there are more parallel things then just MD.

Yeah, that was on the old wiki more than a year ago. I think I might 
have written it based on something I'd seen discussed on one of these 
lists. It's turned out to be wrong... none of the 4.0.5 utilities calls 
an MPI initialization function. I've edited that page suitably.

Mark

On Wed, Oct 14, 2009 at 10:48 AM, Mark Abraham > wrote:

 > Itamar Kass wrote:
 >>
 >> Hi,
 >>
 >> I wonder if there a way to run g_cover in paralel in order to make
 >> things run faster?
 >
 > No. Obviously you can use -dt to reduce the number of frames you analyze.
 >
 >> Also, what analysis programs can run in parallel?
 >
 > None in 4.0.x. Not sure about future plans.
 >
 > Matk
 > ___
 > gmx-users mailing listgmx-users@gromacs.org 

 > http://lists.gromacs.org/mailman/listinfo/gmx-users
 > Please search the archive at http://www.gromacs.org/search before 
posting!
 > Please don't post (un)subscribe requests to the list. Use the www 
interface
 > or send it to gmx-users-requ...@gromacs.org 
.

 > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
 >

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[gmx-users] interpolation for tabulated potential

2009-10-13 Thread LuLanyuan


Hello,
I'm just wondering what interpolation method is used for the tabulated 
potential function in GMX. Since GMX 4, the input table contains potential and 
force, unlike potential and second derivative in GMX 3. Is cubic spline still 
used in GMX 4? If yes, what algorithm is implemented to get second derivative 
needed for cubic spline?
Thanks,
Lanyuan
  
_
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Re: [gmx-users] p0_4238: p4_error: interrupt SIGSEGV: 11




Yongchul Chung wrote:

I think your box is too small. try changing them.



What leads you to this conclusion?  We have no information about the box. 
Presumably, the only box that is "too small" would be one that doesn't satisfy 
the minimum image convention, but grompp fails with a fatal error in that case.


-Justin

On Tue, Oct 13, 2009 at 8:05 PM, Justin A. Lemkul > wrote:




Nilesh Dhumal wrote:

Hello,

I am trying to equilibrate glucose in water using Gromacs
4.0.5 version.  I am geting the error immidiately after the
mdrun starts
Warning: 1-4 interaction between 1 and 18 at distance 3.462 which is
larger than the 1-4 table size 2.400 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
p0_4238:  p4_error: interrupt SIGSEGV: 11
Killed by signal 2.


Have you searched the website?  You would have undoubtedly found this:



http://www.gromacs.org/Documentation/Errors#1-4_interaction_not_within_cut-off

You should also search the list archive.  This problem shows up
weekly, if not daily sometimes.


Is the problem in mdp file?


Nothing seems obviously wrong.

-Justin


Nilesh

Here is my pr.mdp file
title   =  cpeptid position restraining
cpp =  /usr/bin/cpp
constraints =  none
integrator  =  md
dt  =  0.002; ps !
nsteps  =  20  ; total 1.0 ps.
nstcomm =  1
nstxout =  10
nstvout =  1000
nstfout =  0
nstlog  =  10
nstenergy   =  10
nstlist =  10
ns_type =  grid
rlist   =  1.0
coulombtype = PME
vdwtype = cut-off
rcoulomb=  1.0
rvdw=  1.4
fourierspacing  = 0.12
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
; Berendsen temperature coupling is on
Tcoupl = Berendsen
tau_t = 0.1
tc-grps  =system
ref_t =   350
; Pressure coupling is  on
Pcoupl  = Berendsen
pcoupltype  = isotropic
tau_p   =  0.5
compressibility =  4.5e-5
ref_p   =  1.0
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  350.0
gen_seed=  173529







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-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin



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--
Yongchul "Greg" Chung
Graduate Student
Dept. of Chemical Engineering, Case Western Reserve University


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] p0_4238: p4_error: interrupt SIGSEGV: 11

I think your box is too small. try changing them.

On Tue, Oct 13, 2009 at 8:05 PM, Justin A. Lemkul  wrote:

>
>
> Nilesh Dhumal wrote:
>
>> Hello,
>>
>> I am trying to equilibrate glucose in water using Gromacs
>> 4.0.5 version.  I am geting the error immidiately after the mdrun starts
>> Warning: 1-4 interaction between 1 and 18 at distance 3.462 which is
>> larger than the 1-4 table size 2.400 nm
>> These are ignored for the rest of the simulation
>> This usually means your system is exploding,
>> if not, you should increase table-extension in your mdp file
>> or with user tables increase the table size
>> p0_4238:  p4_error: interrupt SIGSEGV: 11
>> Killed by signal 2.
>>
>>
> Have you searched the website?  You would have undoubtedly found this:
>
>
> http://www.gromacs.org/Documentation/Errors#1-4_interaction_not_within_cut-off
>
> You should also search the list archive.  This problem shows up weekly, if
> not daily sometimes.
>
>  Is the problem in mdp file?
>>
>
> Nothing seems obviously wrong.
>
> -Justin
>
>
>  Nilesh
>>
>> Here is my pr.mdp file
>> title   =  cpeptid position restraining
>> cpp =  /usr/bin/cpp
>> constraints =  none
>> integrator  =  md
>> dt  =  0.002; ps !
>> nsteps  =  20  ; total 1.0 ps.
>> nstcomm =  1
>> nstxout =  10
>> nstvout =  1000
>> nstfout =  0
>> nstlog  =  10
>> nstenergy   =  10
>> nstlist =  10
>> ns_type =  grid
>> rlist   =  1.0
>> coulombtype = PME
>> vdwtype = cut-off
>> rcoulomb=  1.0
>> rvdw=  1.4
>> fourierspacing  = 0.12
>> fourier_nx   = 0
>> fourier_ny   = 0
>> fourier_nz   = 0
>> pme_order   = 4
>> ewald_rtol  = 1e-5
>> optimize_fft= yes
>> ; Berendsen temperature coupling is on
>> Tcoupl = Berendsen
>> tau_t = 0.1
>> tc-grps  =system
>> ref_t =   350
>> ; Pressure coupling is  on
>> Pcoupl  = Berendsen
>> pcoupltype  = isotropic
>> tau_p   =  0.5
>> compressibility =  4.5e-5
>> ref_p   =  1.0
>> ; Generate velocites is on at 300 K.
>> gen_vel =  yes
>> gen_temp=  350.0
>> gen_seed=  173529
>>
>>
>>
>>
>>
>>
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>
> ___
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>



-- 
Yongchul "Greg" Chung
Graduate Student
Dept. of Chemical Engineering, Case Western Reserve University
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[gmx-users] Re: Reg: GROMACS Queries



Please keep all GROMACS-related correspondence on the gmx-users list.  I do not 
advertise myself as a private tutor, nor do I claim to have all the answers. 
You stand a much better chance of getting useful information by posting to the list.


The concept of pH in a simulation is a difficult one.  You may find the 
information here useful:


http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation

In one sense, you can protonate residues according to how they would 
predominantly exist at a given pH, but you can't really account for the effects 
of proton transfer between residues.  Protonation states can be assigned when 
running pdb2gmx.


-Justin

Suguna wrote:

Dear Justin,

 

Iam S.Sugunadevi doing my Ph.D. in Korea. Iam very new to this field 
(Molecular Dynamics). I got your ID from GROMACS mailing list.


 

I would like to do MD in different pH values. Kindly, could you guide 
me, where to include that pH values and how?


 


Iam eagerly waiting for your responds.

 


Kindly help me.

 


Thanks in advance.

 


Regards

Sugunadevi.S



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] run g_cover in parallel

2009-10-13 Thread Itamar Kass

Hi,

This is strange, 'cause on the site under installing (using MPI) it is
written "*In GROMACS 4.x, some of the utility programs are also MPI-aware,
but these will only be for compute-intensive utilities (e.g. that
diagonalize large matrices, or calculate autocorrelations, etc.).*".
So I guess there are more parallel things then just MD.

Cheers,
Itamar

On Wed, Oct 14, 2009 at 10:48 AM, Mark Abraham 
wrote:
> Itamar Kass wrote:
>>
>> Hi,
>>
>> I wonder if there a way to run g_cover in paralel in order to make
>> things run faster?
>
> No. Obviously you can use -dt to reduce the number of frames you analyze.
>
>> Also, what analysis programs can run in parallel?
>
> None in 4.0.x. Not sure about future plans.
>
> Matk
> ___
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] p0_4238: p4_error: interrupt SIGSEGV: 11




Nilesh Dhumal wrote:

Hello,

I am trying to equilibrate glucose in water using Gromacs
4.0.5 version.  I am geting the error immidiately after the mdrun starts
Warning: 1-4 interaction between 1 and 18 at distance 3.462 which is
larger than the 1-4 table size 2.400 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
p0_4238:  p4_error: interrupt SIGSEGV: 11
Killed by signal 2.



Have you searched the website?  You would have undoubtedly found this:

http://www.gromacs.org/Documentation/Errors#1-4_interaction_not_within_cut-off

You should also search the list archive.  This problem shows up weekly, if not 
daily sometimes.



Is the problem in mdp file?


Nothing seems obviously wrong.

-Justin


Nilesh

Here is my pr.mdp file
title   =  cpeptid position restraining
cpp =  /usr/bin/cpp
constraints =  none
integrator  =  md
dt  =  0.002; ps !
nsteps  =  20  ; total 1.0 ps.
nstcomm =  1
nstxout =  10
nstvout =  1000
nstfout =  0
nstlog  =  10
nstenergy   =  10
nstlist =  10
ns_type =  grid
rlist   =  1.0
coulombtype = PME
vdwtype = cut-off
rcoulomb=  1.0
rvdw=  1.4
fourierspacing  = 0.12
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
; Berendsen temperature coupling is on
Tcoupl = Berendsen
tau_t = 0.1
tc-grps  =system
ref_t =   350
; Pressure coupling is  on
Pcoupl  = Berendsen
pcoupltype  = isotropic
tau_p   =  0.5
compressibility =  4.5e-5
ref_p   =  1.0
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  350.0
gen_seed=  173529







___
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] p0_4238: p4_error: interrupt SIGSEGV: 11


Nilesh Dhumal wrote:

Hello,

I am trying to equilibrate glucose in water using Gromacs
4.0.5 version.  I am geting the error immidiately after the mdrun starts
Warning: 1-4 interaction between 1 and 18 at distance 3.462 which is
larger than the 1-4 table size 2.400 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
p0_4238:  p4_error: interrupt SIGSEGV: 11
Killed by signal 2.

Is the problem in mdp file?


No, there's something nonphysical about your starting structure, and 
it's blowing up. See 
http://www.gromacs.org/Documentation/Errors#1-4_interaction_not_within_cut-off 
Go and have a look at your structure to start with :-)


Mark


Nilesh

Here is my pr.mdp file
title   =  cpeptid position restraining
cpp =  /usr/bin/cpp
constraints =  none
integrator  =  md
dt  =  0.002; ps !
nsteps  =  20  ; total 1.0 ps.
nstcomm =  1
nstxout =  10
nstvout =  1000
nstfout =  0
nstlog  =  10
nstenergy   =  10
nstlist =  10
ns_type =  grid
rlist   =  1.0
coulombtype = PME
vdwtype = cut-off
rcoulomb=  1.0
rvdw=  1.4
fourierspacing  = 0.12
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
; Berendsen temperature coupling is on
Tcoupl = Berendsen
tau_t = 0.1
tc-grps  =system
ref_t =   350
; Pressure coupling is  on
Pcoupl  = Berendsen
pcoupltype  = isotropic
tau_p   =  0.5
compressibility =  4.5e-5
ref_p   =  1.0
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  350.0
gen_seed=  173529







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[gmx-users] p0_4238: p4_error: interrupt SIGSEGV: 11

2009-10-13 Thread Nilesh Dhumal

Hello,

I am trying to equilibrate glucose in water using Gromacs
4.0.5 version.  I am geting the error immidiately after the mdrun starts
Warning: 1-4 interaction between 1 and 18 at distance 3.462 which is
larger than the 1-4 table size 2.400 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
p0_4238:  p4_error: interrupt SIGSEGV: 11
Killed by signal 2.

Is the problem in mdp file?
Nilesh

Here is my pr.mdp file
title   =  cpeptid position restraining
cpp =  /usr/bin/cpp
constraints =  none
integrator  =  md
dt  =  0.002; ps !
nsteps  =  20  ; total 1.0 ps.
nstcomm =  1
nstxout =  10
nstvout =  1000
nstfout =  0
nstlog  =  10
nstenergy   =  10
nstlist =  10
ns_type =  grid
rlist   =  1.0
coulombtype = PME
vdwtype = cut-off
rcoulomb=  1.0
rvdw=  1.4
fourierspacing  = 0.12
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
; Berendsen temperature coupling is on
Tcoupl = Berendsen
tau_t = 0.1
tc-grps  =system
ref_t =   350
; Pressure coupling is  on
Pcoupl  = Berendsen
pcoupltype  = isotropic
tau_p   =  0.5
compressibility =  4.5e-5
ref_p   =  1.0
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  350.0
gen_seed=  173529







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Re: [gmx-users] run g_cover in parallel


Itamar Kass wrote:

Hi,

I wonder if there a way to run g_cover in paralel in order to make
things run faster?


No. Obviously you can use -dt to reduce the number of frames you analyze.


Also, what analysis programs can run in parallel?


None in 4.0.x. Not sure about future plans.

Matk
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[gmx-users] run g_cover in parallel

2009-10-13 Thread Itamar Kass

Hi,

I wonder if there a way to run g_cover in paralel in order to make
things run faster? Also, what analysis programs can run in parallel?

Best,
Itamar

---

 "In theory, there is no difference between theory and practice. But,
in practice, there is." - Jan L.A. van de Snepscheut

===
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: itamar.k...@med.monash.edu.au

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Re: [gmx-users] What is best way to get multiple chains?


ms wrote:

Hi,

I am a gmx newbie, so please don't bite too much! :)

Learning gmx, I am experimenting with simulations with multiple
identical small chains. What I did was:

- I generated the peptides with pymol
- Generated a .gro with pdb2gmx


This step is "generating a molecular topology". You don't need a .gro - 
it's just a regularized coordinate file produced as a side-effect.



- Used editconf to create translated copies


Try genconf to do the replication. That should remove much of the manual 
labour. You would still probably need to edit in the chain IDs yourself, 
but that's easy work with a script or good editor.



- Stitching them together and creating the complete file, adjusting
numbers etc. manually

It worked well, but the chains are not recognized as *different* chains
-which could be useful. Documentation says I should use another format
like the pdb, but it is a bit sparse on the subject. I think I can use
pdb instead of gro if needed, but does this also work when creating
boxes etc.? Isn't there a way to get chain identifiers in a gro file?
What is best practice?


What do you want the chain identifiers for? I'm not aware of a 
post-pdb2gmx purpose that they might serve.


If your system is N identical peptides in a solvent, then best practice 
for generating a complete .top is to generate one for a single peptide 
in solvent (e.g. pdb2gmx - editconf - genbox). Then generate a 
coordinate file which contains the N peptides' coordinates followed by 
all the solvent (e.g. genconf - genbox). Then edit the [ molecules ] 
section of the original .top to match. Other solutions are possible, but 
require more involved use of pdb2gmx, and might indeed want chain IDs.


Mark
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Re: [gmx-users] major issue with gmx-4.0.3?




XAvier Periole wrote:


Dears,

I recall the report of a major issue in gmx-4.0.3. At the time this
made me put gmx403 on the side of "not to be used versions".

I can not find a trace of it ... anyone would remember anything?


I thought the major problem was with 4.0.1 - it had something broken that caused 
simulations to run something like 50% slower, and hence why it is unavailable 
for download.


There were some issues with the free energy code, missing interactions when 
using TIP4P, I believe, and otherwise small issues with the pull code.  Complete 
release notes are posted on the website:


http://www.gromacs.org/About_Gromacs/Release_Notes/Revisions_in_4.0

-Justin



Thanks,
XAvier.

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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] major issue with gmx-4.0.3?

2009-10-13 Thread XAvier Periole



Dears,

I recall the report of a major issue in gmx-4.0.3. At the time this
made me put gmx403 on the side of "not to be used versions".

I can not find a trace of it ... anyone would remember anything?

Thanks,
XAvier.

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Re: [gmx-users] RMSF reference state?




Pan Wu wrote:

Hi everyone,
Thank you for answering my former questions, it really help me, the 
new gmx-er a lot~

Here is another question about reference state of RMSF.
In the manual, it shows "g_rmsf computes the root mean square 
fluctuation (RMSF, i.e. standard deviation) of atomic positions 
after (optionally) fitting to a reference frame". So in this way, can I 
choose the reference frame from *.tpr file or the coordinate average 
over the whole trajectory? If Gromacs can, how?


I believe the reference structure is taken from whatever structure file is given 
to the -s flag, so in principle you could provide any frame from the trajectory, 
as well as the initial one, or some average structure (from, i.e. g_cluster or 
something similar).


-Justin


Thank you  in advance!

--
Sincerely
=
Pan Wu
Graduate Student in Department of Chemistry
Duke University
124 Science Drive
5301 French Family Science Center
Durham, NC 27708
Phone: (919) 660-1583
=




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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] RMSF reference state?

2009-10-13 Thread Pan Wu

Hi everyone,Thank you for answering my former questions, it really help
me, the new gmx-er a lot~
Here is another question about reference state of RMSF.
In the manual, it shows "g_rmsf computes the root mean square
fluctuation (RMSF, i.e. standard deviation) of atomic positions
after (optionally) fitting to a reference frame". So in this way, can I
choose the reference frame from *.tpr file or the coordinate average over
the whole trajectory? If Gromacs can, how?
Thank you  in advance!

-- 
Sincerely
=
Pan Wu
Graduate Student in Department of Chemistry
Duke University
124 Science Drive
5301 French Family Science Center
Durham, NC 27708
Phone: (919) 660-1583
=
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[gmx-users] Check out my photos on Facebook

2009-10-13 Thread Mohit Kumar Panwar

Hi gmx-users@gromacs.org,

I set up a Facebook profile where I can post my pictures, videos and events and 
I want to add you as a friend so you can see it. First, you need to join 
Facebook! Once you join, you can also create your own profile.

Thanks,
Mohit

To sign up for Facebook, follow the link below:
http://www.facebook.com/p.php?i=1025002649&k=Z6GYY5U4QWTF6BD1QC35XSTQVUIB4XZ1R3CVD&r



Already have an account? Add this email address to your account 
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receive this type of email from Facebook in the future, please click on the 
link below to unsubscribe.
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Facebook's offices are located at 1601 S. California Ave., Palo Alto, CA 94304.

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Re: [gmx-users] What is best way to get multiple chains?




ms wrote:

Hi,

I am a gmx newbie, so please don't bite too much! :)

Learning gmx, I am experimenting with simulations with multiple
identical small chains. What I did was:

- I generated the peptides with pymol
- Generated a .gro with pdb2gmx
- Used editconf to create translated copies
- Stitching them together and creating the complete file, adjusting
numbers etc. manually

It worked well, but the chains are not recognized as *different* chains
-which could be useful. Documentation says I should use another format
like the pdb, but it is a bit sparse on the subject. I think I can use
pdb instead of gro if needed, but does this also work when creating
boxes etc.? Isn't there a way to get chain identifiers in a gro file?
What is best practice?


You can use .pdb format just fine.  There is no requirement that you use .gro, 
and in fact the format specification of .gro does not include a field for chain 
identifier, so no, there is no way to include chain identifiers in a .gro file.


-Justin



Thanks a lot,
Massimo
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Inserting protein in Bilayer

sunny mishra wrote:

Hi Justin,

I have successfully created the lipid bilayer and inserted the protein
inside that but now I feel that before doing all that I would have
placed the water molecules or lipid molecules at some specific point.
I want to create a lipid bilayer in which protein is inserted and on
the top of insertion i need to put the water molecules and then at the
bottom as well. What I don't understand is that how to place the
molecules as per my interest because i am following martini tutorial
and doing everything in CG and that is confusing for me now at this
point that how to put the water molecules or lipid with protein as per
my interest. I hope you got my question.

Thanks for all the previous help and your reply for the same would be
highly appreciable

Use genbox. Please see my tutorial (linked before) and/or:

http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations#Adding_waters_with_genbox

There is a coarse-grain water box that would be a suitable solvent.

-Justin

Thanks,

Sunny

On Sun, Oct 11, 2009 at 5:50 PM, Justin A. Lemkul wrote:

sunny mishra wrote:

Hi Justin,

I have set up the whole system correctly but now at the final step
when I do mdrun it gives me the fatal error by saying that Number of
grid cells is zero. Probably the system and box collapsed.

Then "correctly" is debatable :)

Do you have any idea about this?

Something is unstable in your system. See here:

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

Beyond that, you'll have to describe what you've done as far as energy
minimization and equilibration, and the level of success of each of those
steps.

-Justin

Sunny

On Sun, Oct 11, 2009 at 4:45 PM, sunny mishra
wrote:

Hi Justin,

Thanks for the quick reply. I am also following the martini tutorial
in order to do the CG simulations. Here are the following steps which
I am doing. Please have a look at them.

1) Cleaned the 1SU4.pdb file and renamed it to 1SU4_clean.pdb
2) converted 1SU4_clean.pdb to its CG structure using awk script and
named it to 1SU4_cleancg.pdb
3) Then created the sequence of 1SU4_clean.pdb file and also the .ssd
files.
4) Then using the seq2itp script created the protein.itp file for 1SU4.
5) Now I don't understand after this point what should I do because I
also have to include DSPC molecules. Where should I include them I
mean at which step?
When I make my .top file for the protein do I include DSPC molecules
there or anywhere else? Please let me know

Sunny

On Sun, Oct 11, 2009 at 4:30 PM, Justin A. Lemkul
wrote:

sunny mishra wrote:

Hi All,

I am working on the CG simulations of the proteins and lipid bilayers.
I am confused of how to set up the whole system for simulations. I got
the DSPC lipid bilayer from martini website and I have 1SU4.pdb file
with me. I cleaned the .pdb file and now I want to include the 14 DSPC
molecules in my .pdb file. I don't know if I am going in the right
direction or not. Please let me know how to set up the simulation for
the same if you have some idea. I will appreciate your help.

I wrote a tutorial for atomistic membrane protein systems:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html

It may provide some useful information, since the premise for
constructing
the system is the same. Our web server is currently down due to a power
outage at our University, but I should have everything up and running by
tomorrow.

-Justin

Thanks,

Suny
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Department of Biochemistry
Virginia Tech
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jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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Re: [gmx-users] Advantage of NPT over NVT?

The experimental value of the compressibility of n-alkanes, DMS, and
1-alcohols can be found in following reference document.

http://www.rsc.org/publishing/journals/CP/article.asp?doi=b206425a


On Tue, Oct 13, 2009 at 4:08 PM, Justin A. Lemkul  wrote:

>
>
> Pan Wu wrote:
>
>> Hello everyone,
>>Is there any advantage of using NPT ensemble over NVT? Seems people
>> doing simulation with gromacs like to use NPT (for protein + solvent
>> system). However, for NPT, there is one parameter "compressibility" which is
>> tricky to choose; for NVT, it is so simple.
>>Can anyone give me some suggestion or explanation on this part?
>>
>
> Background reading on statistical mechanics would help :)  Basically, the
> ensemble you choose must represent some conditions, either constant volume
> or constant pressure.
>
> Perhaps you can get some more useful advice about compressibility if you
> describe your system.  For aqueous systems (as the manual advises), the
> compressibility of water is sufficient.  For other media, compressibility
> data can be found in a number of sources, i.e. The Handbook of Chemistry and
> Physics.
>
> -Justin
>
> Thank you very much in advance!
>>
>> Sincerely
>> Pan Wu
>>
>>
>> 
>>
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>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>
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-- 
Yongchul "Greg" Chung
Graduate Student
Dept. of Chemical Engineering, Case Western Reserve University
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Re: [gmx-users] Advantage of NPT over NVT?




Pan Wu wrote:

Hello everyone,
Is there any advantage of using NPT ensemble over NVT? Seems people 
doing simulation with gromacs like to use NPT (for protein + solvent 
system). However, for NPT, there is one parameter "compressibility" 
which is tricky to choose; for NVT, it is so simple.

Can anyone give me some suggestion or explanation on this part?


Background reading on statistical mechanics would help :)  Basically, the 
ensemble you choose must represent some conditions, either constant volume or 
constant pressure.


Perhaps you can get some more useful advice about compressibility if you 
describe your system.  For aqueous systems (as the manual advises), the 
compressibility of water is sufficient.  For other media, compressibility data 
can be found in a number of sources, i.e. The Handbook of Chemistry and Physics.


-Justin


Thank you very much in advance!

Sincerely
Pan Wu




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--


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ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
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jalemkul[at]vt.edu | (540) 231-9080
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Re: [gmx-users] grompp output on terminal




Lum Nforbi wrote:

Hello everyone,
   I had written earlier today about my concern involving grompp. I am 
trying to minimize the energy of a pure water system using grompp: 
grompp -f waters.mdp -c waters_b.gro -p water.top -o watersinput.tpr

and part of the output on the terminal is as follows:

  Analysing residue names:
  Opening library file 
/usr/local/gromacs/share/gromacs/top/aminoacids.dat

  There are:  2000  OTHER residues
  There are: 0PROTEIN residues
  There are: 0DNA residues

  NOTE 1 [file aminoacids.dat, line 1]:
  The optimal PME mesh load for parallel simulations is below 0.5
  and for highly parallel simulations between 0.25 and 0.33,
  for higher performance, increase the cut-off and the PME grid spacing

The problem is I am not specifying any aminoacid file and I am not doing 
a parallel run, but the aminoacid.dat file is being opened and the 
program assumes that I am doing a parallel run. Is this the way it 
should be, and will this affect my run results?
  Please help me out and be patient with me as I am still learning 
gromacs.


The aminoacids.dat is a generic input file that tells grompp what is protein and 
what is not.  In your case, it simply doesn't matter.


The note about PME is also standard output, since parallel runs are quite 
common, this is useful information.  There is no way for grompp to know if you 
are going to be running in parallel, but it's simply providing you useful 
information.


Basically, all the output is entirely normal.  As long as grompp isn't spitting 
out warnings/errors, you should be fine to continue.


-Justin


Thanks,
Lum





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Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] eliminating forces on certain direction

2009-10-13 Thread 吴鹏

Hi Mark,

What you said reminds me to think deeply about my speculation. Thanks for
your remind and I hope to discuss it with you when I get some ideas on that.

Peng Wu

On Tue, Oct 13, 2009 at 10:02 AM, Mark Abraham wrote:

> 吴鹏 wrote:
>
>> Hi Mark,
>>
>> Haha. Yes, your words is right. My objective is to study the interaction
>> between ions and walls. I think the ions may be attached in the wall so the
>> velocity getten from MD simulation is always bigger than the continuum
>> theory's prediction. So I want to build a simulation on which ion can not be
>> attached to the wall. My methods is to reduce the interaction of wall and
>> ions on flow direction. That's my obeject. Any suggestion on that? Thanks in
>> advance.
>>
>
> Probably not, but you'd have to use more precise descriptions than
> "attached in/to the wall" :-) Basically any time you make some perturbation
> to the physics of some force field, you would need to do a lot of spadework
> proving that you haven't produced a (garbage in => garbage out) system.
>
> Mark
>
>  On Mon, Oct 12, 2009 at 8:45 PM, Mark Abraham 
> > mark.abra...@anu.edu.au>> wrote:
>>
>>?? wrote:
>>
>>Hi GMX users,
>>
>>I am doing a modified simulation which requires to eliminate an
>>interaction at certain direction while remain the interaction at
>>other directions. Since the itp files contain the C6 C12 of the
>>interaction, it is impossible to only remain the interaction a
>>one direction while eliminating the interaction at other
>>directions. I am thinking of hacking the code while I have no
>>idea of how to do it. Any suggestions on that? Thanks in advance.
>>
>>
>>Start by describing your actual objective in general terms, and not
>>pre-supposing the form of the solution (i.e. manually changing
>>certain interactions). The above sounds like a recipe for disaster,
>>even if you could make it work :-)
>>
>>Mark
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>>
>> 
>>
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[gmx-users] What is best way to get multiple chains?

2009-10-13 Thread ms

Hi,

I am a gmx newbie, so please don't bite too much! :)

Learning gmx, I am experimenting with simulations with multiple
identical small chains. What I did was:

- I generated the peptides with pymol
- Generated a .gro with pdb2gmx
- Used editconf to create translated copies
- Stitching them together and creating the complete file, adjusting
numbers etc. manually

It worked well, but the chains are not recognized as *different* chains
-which could be useful. Documentation says I should use another format
like the pdb, but it is a bit sparse on the subject. I think I can use
pdb instead of gro if needed, but does this also work when creating
boxes etc.? Isn't there a way to get chain identifiers in a gro file?
What is best practice?

Thanks a lot,
Massimo
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Re: [gmx-users] Is there something wrong with the Gromacs site?

ditto. I hope they are upgrading the server.

On Tue, Oct 13, 2009 at 11:29 AM, Michael Shirts  wrote:

> I'm getting:
>
> Site settings could not be loaded
>
> We were unable to locate the API to request site settings. Please see
> below for debugging information.
>
> HTTP Response Status Code: 500
>
> The API says: wiki 'www.gromacs.org' has failed to initialize or did
> not start up properly: Initialization exception:
> MySql.Data.MySqlClient.MySqlException: Too many connections at
> MySql.Data.MySqlClient.MySqlStream.OpenPacket () [0x0] at
> MySql.Data.MySqlClient.NativeDriver.Open () [0x0] at
> MySql.Data.MySqlClient.Driver.Create
> (MySql.Data.MySqlClient.MySqlConnectionStringBuilder settings)
> [0x0] at MySql.Data.MySqlClient.MySqlPool..ctor
> (MySql.Data.MySqlClient.MySqlConnectionStringBuilder settings)
> [0x0] at MySql.Data.MySqlClient.MySqlPoolManager.GetPool
> (MySql.Data.MySqlClient.MySqlConnectionStringBuilder settings)
> [0x0] at MySql.Data.MySqlClient.MySqlConnection.Open (Boolean
> allowPooled) [0x0]
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-- 
Yongchul "Greg" Chung
Graduate Student
Dept. of Chemical Engineering, Case Western Reserve University
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[gmx-users] Is there something wrong with the Gromacs site?

2009-10-13 Thread Michael Shirts

I'm getting:

Site settings could not be loaded

We were unable to locate the API to request site settings. Please see
below for debugging information.

HTTP Response Status Code: 500

The API says: wiki 'www.gromacs.org' has failed to initialize or did
not start up properly: Initialization exception:
MySql.Data.MySqlClient.MySqlException: Too many connections at
MySql.Data.MySqlClient.MySqlStream.OpenPacket () [0x0] at
MySql.Data.MySqlClient.NativeDriver.Open () [0x0] at
MySql.Data.MySqlClient.Driver.Create
(MySql.Data.MySqlClient.MySqlConnectionStringBuilder settings)
[0x0] at MySql.Data.MySqlClient.MySqlPool..ctor
(MySql.Data.MySqlClient.MySqlConnectionStringBuilder settings)
[0x0] at MySql.Data.MySqlClient.MySqlPoolManager.GetPool
(MySql.Data.MySqlClient.MySqlConnectionStringBuilder settings)
[0x0] at MySql.Data.MySqlClient.MySqlConnection.Open (Boolean
allowPooled) [0x0]
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[gmx-users] grompp output on terminal

2009-10-13 Thread Lum Nforbi

Hello everyone,
   I had written earlier today about my concern involving grompp. I am
trying to minimize the energy of a pure water system using grompp: grompp -f
waters.mdp -c waters_b.gro -p water.top -o watersinput.tpr
and part of the output on the terminal is as follows:

  Analysing residue names:
  Opening library file /usr/local/gromacs/share/gromacs/top
/aminoacids.dat
  There are:  2000  OTHER residues
  There are: 0PROTEIN residues
  There are: 0DNA residues

  NOTE 1 [file aminoacids.dat, line 1]:
  The optimal PME mesh load for parallel simulations is below 0.5
  and for highly parallel simulations between 0.25 and 0.33,
  for higher performance, increase the cut-off and the PME grid spacing

The problem is I am not specifying any aminoacid file and I am not doing a
parallel run, but the aminoacid.dat file is being opened and the program
assumes that I am doing a parallel run. Is this the way it should be, and
will this affect my run results?
  Please help me out and be patient with me as I am still learning
gromacs.
Thanks,
Lum
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Re: [gmx-users] eliminating forces on certain direction


吴鹏 wrote:

Hi Mark,

Haha. Yes, your words is right. My objective is to study the interaction 
between ions and walls. I think the ions may be attached in the wall so 
the velocity getten from MD simulation is always bigger than the 
continuum theory's prediction. So I want to build a simulation on which 
ion can not be attached to the wall. My methods is to reduce the 
interaction of wall and ions on flow direction. That's my obeject. Any 
suggestion on that? Thanks in advance.


Probably not, but you'd have to use more precise descriptions than 
"attached in/to the wall" :-) Basically any time you make some 
perturbation to the physics of some force field, you would need to do a 
lot of spadework proving that you haven't produced a (garbage in => 
garbage out) system.


Mark

On Mon, Oct 12, 2009 at 8:45 PM, Mark Abraham > wrote:


?? wrote:

Hi GMX users,

I am doing a modified simulation which requires to eliminate an
interaction at certain direction while remain the interaction at
other directions. Since the itp files contain the C6 C12 of the
interaction, it is impossible to only remain the interaction a
one direction while eliminating the interaction at other
directions. I am thinking of hacking the code while I have no
idea of how to do it. Any suggestions on that? Thanks in advance.


Start by describing your actual objective in general terms, and not
pre-supposing the form of the solution (i.e. manually changing
certain interactions). The above sounds like a recipe for disaster,
even if you could make it work :-)

Mark
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Re: [gmx-users] Opening aminoacids.dat file during grommp


Lum Nforbi wrote:

Hello all,
 
I am running grommp which kind of goes "successfully" but I am a little 
concerned about the fact that one of the messages in the terminal says 
"opening aminoacids.dat file" and in another message says "OTHER: 2000 
residues found." I guess this 2000 is refering to the  2000 water 
molecules in my system since I am using just pure water and the command 
line I am using is:


grompp -f waters.mdp -c waters2000_b.gro -p waters2000.top -o 
watersinput.tpr


 I did not specify an amino acid file and I am not sure where that 
statement "opening aminoacids.dat file" is coming from. Will this affect 
my run?


That's normal - this file merely names residues that grompp should 
consider to be "protein". You have none, which doesn't matter.


Mark
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Re: [gmx-users] protein domain separate


hazizian wrote:
Hi 
I want to do MD on a two-domain protein (Protein A, Protein B). After doning 
position restranit for 20 ps, the final structure separated. How could I 
keep these 2 domain close to each other during whole MD run.


Check that they're not separated because of a PBC artefact (try trjconv 
-compact or something). If the positions were really restrained, they 
can't actually have separated.


Mark
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Re: [gmx-users] eliminating forces on certain direction

2009-10-13 Thread 吴鹏

Hi Mark,

Haha. Yes, your words is right. My objective is to study the interaction
between ions and walls. I think the ions may be attached in the wall so the
velocity getten from MD simulation is always bigger than the continuum
theory's prediction. So I want to build a simulation on which ion can not be
attached to the wall. My methods is to reduce the interaction of wall and
ions on flow direction. That's my obeject. Any suggestion on that? Thanks in
advance.

Peng Wu

On Mon, Oct 12, 2009 at 8:45 PM, Mark Abraham wrote:

> ?? wrote:
>
>> Hi GMX users,
>>
>> I am doing a modified simulation which requires to eliminate an
>> interaction at certain direction while remain the interaction at other
>> directions. Since the itp files contain the C6 C12 of the interaction, it is
>> impossible to only remain the interaction a one direction while eliminating
>> the interaction at other directions. I am thinking of hacking the code while
>> I have no idea of how to do it. Any suggestions on that? Thanks in advance.
>>
>
> Start by describing your actual objective in general terms, and not
> pre-supposing the form of the solution (i.e. manually changing certain
> interactions). The above sounds like a recipe for disaster, even if you
> could make it work :-)
>
> Mark
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[gmx-users] Opening aminoacids.dat file during grommp

2009-10-13 Thread Lum Nforbi

Hello all,

I am running grommp which kind of goes "successfully" but I am a little
concerned about the fact that one of the messages in the terminal says
"opening aminoacids.dat file" and in another message says "OTHER: 2000
residues found." I guess this 2000 is refering to the  2000 water molecules
in my system since I am using just pure water and the command line I am
using is:

grompp -f waters.mdp -c waters2000_b.gro -p waters2000.top -o
watersinput.tpr
 I did not specify an amino acid file and I am not sure where that statement
"opening aminoacids.dat file" is coming from. Will this affect my run?
Please help me out.

Lum
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Re: [gmx-users] Advantage of NPT over NVT?

2009-10-13 Thread Tsjerk Wassenaar

Hi,

In addition to the remarks of Ran and Mark, also note that with NVT
the density of your system may change significantly and artificially,
relating to changes in your protein. This in turn affects the dynamics
of your protein, which should be considered an artefact of NVT
simulations.

Cheers,

Tsjerk

On Tue, Oct 13, 2009 at 8:46 AM, Ran Friedman  wrote:
> Hi,
>
> The simplest ensemble is NVE. Historically, NVT came later to allow
> simulations in constant temperature which seem to be more realistic from an
> experimental point of view. However, experiments are usually performed under
> constant pressure and temperature, which is the reason for people to choose
> NPT.
>
> Parameters that deal with a thermostat and barostat are not straightforward
> to choose - there have been a lot of posts on this list about it. Even NVT
> is not simple.
>
> Ran.
>
> --
> --
> Ran Friedman
> Postdoctoral Fellow
> Computational Structural Biology Group (A. Caflisch)
> Department of Biochemistry
> University of Zurich
> Winterthurerstrasse 190
> CH-8057 Zurich, Switzerland
> Tel. +41-44-639
> Email: r.fried...@bioc.unizh.ch
> Skype: ran.friedman
> --
>
> Pan Wu wrote:
>
> Hello everyone,
>     Is there any advantage of using NPT ensemble over NVT? Seems people
> doing simulation with gromacs like to use NPT (for protein + solvent
> system). However, for NPT, there is one parameter "compressibility" which is
> tricky to choose; for NVT, it is so simple.
>     Can anyone give me some suggestion or explanation on this part?
>     Thank you very much in advance!
> Sincerely
> Pan Wu
>
> 
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-- 
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Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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[gmx-users] protein domain separate

2009-10-13 Thread hazizian

Hi 
I want to do MD on a two-domain protein (Protein A, Protein B). After doning 
position restranit for 20 ps, the final structure separated. How could I 
keep these 2 domain close to each other during whole MD run.
Thank you in advance. 

--
Tehran University of Medical Sciences
www.tums.ac.ir


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Re: [gmx-users] Advantage of NPT over NVT?

2009-10-13 Thread Ran Friedman

Hi,

The simplest ensemble is NVE. Historically, NVT came later to allow
simulations in constant temperature which seem to be more realistic from
an experimental point of view. However, experiments are usually
performed under constant pressure and temperature, which is the reason
for people to choose NPT.

Parameters that deal with a thermostat and barostat are not
straightforward to choose - there have been a lot of posts on this list
about it. Even NVT is not simple.

Ran.

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Pan Wu wrote:
> Hello everyone,
> Is there any advantage of using NPT ensemble over NVT? Seems
> people doing simulation with gromacs like to use NPT (for protein +
> solvent system). However, for NPT, there is one parameter
> "compressibility" which is tricky to choose; for NVT, it is so simple.
> Can anyone give me some suggestion or explanation on this part?
> Thank you very much in advance!
>
> Sincerely
> Pan Wu
>
> 
>
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Re: [gmx-users] g_hbond and fluor

2009-10-13 Thread Ran Friedman

David van der Spoel wrote:
> Alvaro Cortes wrote:
>> Hi all.
>>
>> I'm new at the list so i don't know if something similar has been
>> discussed before.
>> I tried to search in the archives, but i can't find something similar.
>>
>> I have a doubt about g_hbond and fluor acceptors. As i can see in the
>> code, no parsing of F atoms is done in search_acceptors function in
>> gmx_hbond.c, so i added "|| ((*top->atoms.atomname[n])[0] == 'F') ||"
>> between oxygen and nitrogen parsing. This results in an increase of
>> the number of hbonds reported by the program but i dont know if this
>> little change  is enough or even correct.
>>
>> Someone can bring me light in this stuff?
>
> I think it should be correct. Obviously it would be good to be more
> flexible without the need for user programming. In some contexts one
> might want to look for C-H ... 0 bonds as well and even N-H ...
> Aromatic interactions.
A bit off topic from the fluor-related issue, but if you modify g_hbond,
maybe it makes sense to disable nitogen atoms from being acceptors per
default. I don't think having nitrogen acceptors is very common.
>
>>
>> Thank you in advance.
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Re: [gmx-users] Advantage of NPT over NVT?


Pan Wu wrote:

Hello everyone,
Is there any advantage of using NPT ensemble over NVT?


Sure. Most experimental data is measured from NPT. If using REMD, you 
avoid non-physical pressures at high temperature.


 Seems people 
doing simulation with gromacs like to use NPT (for protein + solvent 
system). However, for NPT, there is one parameter "compressibility" 
which is tricky to choose; 


I don't think it is intrinsically tricky. See discussion in manual 
section 3.4.6.


Mark
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Re: [gmx-users] Inserting protein in Bilayer