[gmx-users] Shell MD

[yiran870804]

Dear sir： 
  
Thank you for reading my letter.  
I have a few problems  in Shell MD

   . I have set the parameter of Shell MD as the Gromacs manual   in my 
*.mdp file. 

emtol:10.0
niter:20
fcstep:0

But the result is the same with the traditilnal MD.

Whether the Gromacs can not finish Shell MD?

I hope to obtain your help. 
Your prompt attention to this letter would be highly appreciated. 
 Thanks a lot. 
  

 Liyan

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Re: [gmx-users] Shell MD

[David van der Spoel]

On 2011-11-06 12:23, yiran870804 wrote:

*Dear sir： *

**

*Thank you for reading my letter. *

*I have a few problems in Shell MD

 . I have set the parameter of Shell MD as the Gromacs manualin my
*.mdp file. *

_/emtol:10.0

use 0.001 instead.
one processor only for the time being.


niter:20
fcstep:0/_

*But the result is the same with the traditilnal MD.

be more precise please.


Whether the Gromacs can not finish Shell MD?

have you defined shells? try e.g. the sw.itp file provided with gromacs.


I hope to obtain your help. *

*Your prompt attention to this letter would be highly appreciated. *

*Thanks a lot. *

**

*Liyan
*







--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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[gmx-users] hi

[X Rules]

gmx you really should look into this http://www2.worldnews13now.com/1/ see ya
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RE: [gmx-users] Regarding Table Extension

[Dallas Warren]

Might I suggest you actually state what you don't understand.  Otherwise you 
are leaving an open ended question for people to respond to, which they are 
unlikely to do so.  The more specific and more detail you put into your 
question, the more likely you are to get some useful assistance.

"table-extension = 20 ; (nm) !IMPORTANT! Set this so that rvdw + 
table-extension equals half of the box's longest diagonal."

Are you aware of the situation to which that sample .mdp file is used?  Is that 
situation applicable for what you are doing?

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Ravi Kumar Venkatraman
Sent: Saturday, 5 November 2011 8:13 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] Regarding Table Extension

Dear All,
 This is the site where they have mentioned like the sum of the 
longest diagnol of the box + rlist = table extension

http://smog.ucsd.edu/MDP_sample.html

Further whatever that was mentioned in the manual I could not understand. I 
kindly request any one of you to explain me the same.

Thank you

With Regards,
Ravi Kumar Venkatraman,
IPC Dept., IISc,
Bangalore, INDIA.

+91-9686933963.
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Re: [gmx-users] Regarding Table Extension

[cuong nguyen]

Dear,

I would like to create a solution of mix substances (hexanol and octanol)
in water. I got top files and gro files of these alcohols from PRODRG
server. However I do not know how to mix these top file to create topol.top
file for this mixture.

Please help me.

Thank you very much.

Best regards,

Cuong

2011/11/7 Dallas Warren 

>  Might I suggest you actually state what you don’t understand.  Otherwise
> you are leaving an open ended question for people to respond to, which they
> are unlikely to do so.  The more specific and more detail you put into your
> question, the more likely you are to get some useful assistance.
>
> ** **
>
> “table-extension = 20 ; (nm) !IMPORTANT! Set this so that rvdw +
> table-extension equals half of the box's longest diagonal.”
>
> ** **
>
> Are you aware of the situation to which that sample .mdp file is used?  Is
> that situation applicable for what you are doing?
>
> ** **
>
> Catch ya,
>
> Dr. Dallas Warren
>
> Medicinal Chemistry and Drug Action
>
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.war...@monash.edu
>
> +61 3 9903 9304
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail. 
>
> ** **
>
> *From:* gmx-users-boun...@gromacs.org [mailto:
> gmx-users-boun...@gromacs.org] *On Behalf Of *Ravi Kumar Venkatraman
> *Sent:* Saturday, 5 November 2011 8:13 PM
> *To:* gmx-users@gromacs.org
> *Subject:* [gmx-users] Regarding Table Extension
>
> ** **
>
> *Dear All,
>  This is the site where they have mentioned like the sum of
> the longest diagnol of the box + rlist = table extension
>
> http://smog.ucsd.edu/MDP_sample.html
>
> Further whatever that was mentioned in the manual I could not understand.
> I kindly request any one of you to explain me the same.
>
> Thank you*
>
> *With Regards,
> Ravi Kumar Venkatraman,
> IPC Dept., IISc,
> Bangalore, INDIA.
>
> +91-9686933963.*
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
>



-- 
Nguyen Van Cuong
PhD student - Curtin University of Technology
Mobile: (+61) 452213981
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[gmx-users] how to make topol.top file for mixed solution

[cuong nguyen]

Dear,

I would like to create a solution of mix substances (hexanol and octanol)
in water. I got top files and gro files of these alcohols from PRODRG
server. However I do not know how to mix these top file to create topol.top
file for this mixture.

Please help me.

Thank you very much.

Best regards,

Cuong

Nguyen Van Cuong
PhD student - Curtin University of Technology
Mobile: (+61) 452213981
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Re: [gmx-users] how to make topol.top file for mixed solution

[Justin A. Lemkul]

cuong nguyen wrote:

Dear,

I would like to create a solution of mix substances (hexanol and 
octanol) in water. I got top files and gro files of these alcohols from 
PRODRG server. However I do not know how to mix these top file to create 
topol.top file for this mixture.




Please read the tutorial:

http://www.gromacs.org/Documentation/Tutorials#Heterogeneous_Systems

-Justin


Please help me.

Thank you very much.

Best regards,

Cuong

Nguyen Van Cuong
PhD student - Curtin University of Technology
Mobile: (+61) 452213981
 



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] how to make topol.top file for mixed solution

[Justin A. Lemkul]

Justin A. Lemkul wrote:



cuong nguyen wrote:

Dear,

I would like to create a solution of mix substances (hexanol and 
octanol) in water. I got top files and gro files of these alcohols 
from PRODRG server. However I do not know how to mix these top file to 
create topol.top file for this mixture.




Please read the tutorial:

http://www.gromacs.org/Documentation/Tutorials#Heterogeneous_Systems



Also possibly useful:

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

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Regarding Table Extension

[Justin A. Lemkul]

Please do not double-post and do not hijack existing threads with unrelated 
topics.

-Justin

cuong nguyen wrote:

Dear,

I would like to create a solution of mix substances (hexanol and 
octanol) in water. I got top files and gro files of these alcohols from 
PRODRG server. However I do not know how to mix these top file to create 
topol.top file for this mixture.


Please help me.

Thank you very much.

Best regards,

Cuong

2011/11/7 Dallas Warren >


Might I suggest you actually state what you don’t understand. 
Otherwise you are leaving an open ended question for people to

respond to, which they are unlikely to do so.  The more specific and
more detail you put into your question, the more likely you are to
get some useful assistance.

__ __

“table-extension = 20 ; (nm) !IMPORTANT! Set this so that rvdw +
table-extension equals half of the box's longest diagonal.”

__ __

Are you aware of the situation to which that sample .mdp file is
used?  Is that situation applicable for what you are doing?

__ __

Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu 

+61 3 9903 9304 
-
When the only tool you own is a hammer, every problem begins to
resemble a nail. 

__ __

*From:* gmx-users-boun...@gromacs.org

[mailto:gmx-users-boun...@gromacs.org
] *On Behalf Of *Ravi Kumar
Venkatraman
*Sent:* Saturday, 5 November 2011 8:13 PM
*To:* gmx-users@gromacs.org 
*Subject:* [gmx-users] Regarding Table Extension

__ __

*Dear All,
 This is the site where they have mentioned like the sum
of the longest diagnol of the box + rlist = table extension

http://smog.ucsd.edu/MDP_sample.html

Further whatever that was mentioned in the manual I could not
understand. I kindly request any one of you to explain me the same.

Thank you*

*With Regards,
Ravi Kumar Venkatraman,
IPC Dept., IISc,
Bangalore, INDIA.

+91-9686933963 .*


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.
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--
Nguyen Van Cuong
PhD student - Curtin University of Technology
Mobile: (+61) 452213981
 



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] how to make topol.top file for mixed solution

[cuong nguyen]

Dear,

Thanks a lot Justin. I created a box containing mixed solution of 20
hexanol molecues and 20 octanol molecules in water. However, when I run
grompp and mdrun commands, gromacs noticed errors with the topol.top file
for this mixed system.

So please help me to create a suitable topol.top file to this system.

Thanks a lot.

Best regards,


Cuong

2011/11/7 Justin A. Lemkul 

>
>
> Justin A. Lemkul wrote:
>
>>
>>
>> cuong nguyen wrote:
>>
>>> Dear,
>>>
>>> I would like to create a solution of mix substances (hexanol and
>>> octanol) in water. I got top files and gro files of these alcohols from
>>> PRODRG server. However I do not know how to mix these top file to create
>>> topol.top file for this mixture.
>>>
>>>
>> Please read the tutorial:
>>
>> http://www.gromacs.org/**Documentation/Tutorials#**Heterogeneous_Systems
>>
>>
> Also possibly useful:
>
> http://www.gromacs.org/**Documentation/How-tos/Mixed_**Solvents
>
> -Justin
>
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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
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> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
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> Can't post? Read 
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>



-- 
Nguyen Van Cuong
PhD student - Curtin University of Technology
Mobile: (+61) 452213981
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[gmx-users] refcoord_scaling

[khuchtumur bumerdene]

Hi,
I have a question about refcoord_scaling option and its role in pressure
coupling. What I'm currently doing is just running the lysozyme tutorial on
my own protein.
I've so far had successful runs when equilibrating on my own machine, which
is currently running gmx4.5.3. NPT came to a stable average of ~1.0 bar.
But when I do it on the cluster with gmx4.5.5, grompp gives the following
error:

WARNING 1 [file npt.mdp]:
  You are using pressure coupling with absolute position restraints, this
  will give artifacts. Use the refcoord_scaling option.

My npt.mdp file is as follows (straight from the tutorial at this stage):

define  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 15 ; 2 * 15 = 300 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 100   ; save coordinates every 0.2 ps
nstvout = 100   ; save velocities every 0.2 ps
nstenergy   = 100   ; save energies every 0.2 ps
nstlog  = 100   ; update log file every 0.2 ps
; Bond parameters
continuation= yes   ; Restarting after NVT
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
rvdw= 1.0   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein   ; two coupling groups - more
accurate
tau_t   = 0.1   0.1 ; time constant, in ps
ref_t   = 300   300 ; reference temperature, one for each
group, in K
; Pressure coupling is on
pcoupl  = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype  = isotropic ; uniform scaling of box vectors
tau_p   = 2.0   ; time constant, in ps
ref_p   = 1.0   ; reference pressure, in bar
compressibility = 4.5e-5; isothermal compressibility of water,
bar^-1
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no; Velocity generation is off


The only change I made is the nsteps as my box is bigger and thus has more
waters in it.

So after reading the warning I tried to find some info on the
refcoord_scaling, which the only information found by my feeble attempts
were from the mdp options and the manual, which states:

*refcoord_scaling:* *no*The reference coordinates for position restraints
are not modified. Note that with this option the virial and pressure will
depend on the absolute positions of the reference coordinates.*all*The
reference coordinates are scaled with the scaling matrix of the pressure
coupling.*com*Scale the center of mass of the reference coordinates with
the scaling matrix of the pressure coupling. The vectors of each reference
coordinate to the center of mass are not scaled. Only one COM is used, even
when there are multiple molecules with position restraints. For calculating
the COM of the reference coordinates in the starting configuration,
periodic boundary conditions are not taken into account. I don't quite
understand this completely, is the option there to change the coordinates
of the solute as the box size changes, where the 'all' option changes the
coordinates of every atom and the com only changes the coordinates of the
solute com? Please correct me on this.
So before posting this question I ran a few npt equilibrations with the all
and com options chosen with parrinello-rahman from 100 ps, to 300 ps, and
to 1000 ps. All with 10 different initial velocities from the nvt. The
reason for increasing time is that the equilibration did not reach the
target 1 bar and ended at averages of 4-7 bars for the 10 equilibrations.
The oscillation was comparable to the graph seen on the lysozyme tutorial
between 0-400.
So I tried running berendsen instead of parrinello rahman as the manual
says it should help me get to the target pressure better and I can follow
up with parrinello-rahman. But the pressure still didn't reach the target
pressure.

So the questions are,
- is my naive understanding of the refcoord_scaling correct? if not will
you help explain it to m