Re: [gmx-users] velacc & box of water

[Justin A. Lemkul]

Jamie Seyed wrote:

Hi Justin,
But this seems that did not change the number of molecule in the output 
(only the volume and density are changing) and it seems that -maxsol has 
not been used... my full command

"genbox -cp spc216.gro -maxsol 500 -o out.gro -p topol.top -box 4 4 4"
if I change 500 to any thing else the result is the same and changing 4 
4 4 to any thing else will change the volume and density...


When simultaneously specifying -maxsol and -box, the two must work in harmony. 
A smaller box may not fit 500 molecules, and trying a larger number of molecules 
may not fit in a fixed 4x4x4 nm box.  The command I used that worked was:


genbox -cs spc216.gro -maxsol 500 -o out.gro -box 5 5 5

Note that this gives a weird output configuration, probably because the box is 
not appropriate, but at least its a template of a command that should, in 
theory, work.


Alternatively, you can use the editconf/genbox combination to define a box and 
center the solute (which is water) with editconf -c, then fill the box with 
genbox, where -cp indeed specifies the solute (water) and provides solvent 
(water again!) with -cs.


-Justin


I got confused... I appreciate any hint on that/Thanks/Jamie

On Sun, Oct 11, 2009 at 2:07 PM, Jamie Seyed > wrote:


Thanks Justin,
As I understood -cp is for solute and -cs is for solvent... in this
case I thought that small created volume of water are plying as
solute... and then genbox should fill the box...
Anyways thank you :-)

On Sun, Oct 11, 2009 at 2:01 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote:



Jamie Seyed wrote:

Oh, I just changed the [-cs spc216.gro] to [-cp spc216.gro]
and this is working normally...??!! Do you have any idea?


Oops, I hadn't seen that before.  That is what you should do.
 The -cp flag is the coordinate file that should have solvent
added to it, and that's what you're after, isn't it?

-Justin

On Sun, Oct 11, 2009 at 1:52 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   Jamie Seyed wrote:

   I converted  spc216.pdb to gro using editconf. SO
they must be the


   I suppose that's fine, I just don't see all the need for
   interconverting file formats.  It just opens up the
possibility of
   more errors if you don't keep track of what you're doing :)


   same(?). The version is 4.0.5 ...it was fine
before... yes ran
   it just now for fws tuto... how long it takes time in
your machine?


   I have the same version.  The commands you showed
completed in just
   a fraction of a second, like most simple solvation
procedures.

   -Justin


   On Sun, Oct 11, 2009 at 1:33 PM, Justin A. Lemkul
   mailto:jalem...@vt.edu>
>
   

>
   
>>
   >
   

Re: [gmx-users] velacc & box of water

[Justin A. Lemkul]

Jamie Seyed wrote:
Oh, I just changed the [-cs spc216.gro] to [-cp spc216.gro] and this is 
working normally...??!! Do you have any idea?




Oops, I hadn't seen that before.  That is what you should do.  The -cp flag is 
the coordinate file that should have solvent added to it, and that's what you're 
after, isn't it?


-Justin

On Sun, Oct 11, 2009 at 1:52 PM, Justin A. Lemkul > wrote:




Jamie Seyed wrote:

I converted  spc216.pdb to gro using editconf. SO they must be the


I suppose that's fine, I just don't see all the need for
interconverting file formats.  It just opens up the possibility of
more errors if you don't keep track of what you're doing :)


same(?). The version is 4.0.5 ...it was fine before... yes ran
it just now for fws tuto... how long it takes time in your machine?


I have the same version.  The commands you showed completed in just
a fraction of a second, like most simple solvation procedures.

-Justin


On Sun, Oct 11, 2009 at 1:33 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   Jamie Seyed wrote:

   Hi Justin,
   yes resize.gro is a created file from editconf which has box
   size of  5.05918 on the last line
   my command was "editconf -bt cubic -f spc216.pdb -o
resize.gro -d 1"


   Do you actually have separate spc216.pdb and spc216.gro
files?  Just
   trying to make sure this actually worked.


   and for second command I changed 1 to 5 but it still stops in
   the same point. I am trying to examine 2 methods that you
& Mark
   suggested me to


   Very weird.  Both of your commands worked on my machine.  What
   version of Gromacs are you using?  Does genbox work for other
systems?

   -Justin

   create a box of water.../Many Thanks/Jamie

   On Sun, Oct 11, 2009 at 12:54 PM, Justin A. Lemkul
   mailto:jalem...@vt.edu>
>
   
 >
    >>
  
   > 
   

  wrote:

 Thanks to Justin & Mark for answering my second
   question...
 Could any one give me a hint on my first
question that
   I copy
  it again?
 --about g_velacc and calculating the diffusion
   constant from
  that.
 In mailing list people say that we need to
divide it
   by mass
  squared
 and 1/3. Then I found another recent post that
said it
   has been
 included in the code... Would you please
clarify this
   that if
  I

Re: [gmx-users] velacc & box of water

[Jamie Seyed]

Oh, I just changed the [-cs spc216.gro] to [-cp spc216.gro] and this is
working normally...??!! Do you have any idea?

On Sun, Oct 11, 2009 at 1:52 PM, Justin A. Lemkul  wrote:

>
>
> Jamie Seyed wrote:
>
>> I converted  spc216.pdb to gro using editconf. SO they must be the
>>
>
> I suppose that's fine, I just don't see all the need for interconverting
> file formats.  It just opens up the possibility of more errors if you don't
> keep track of what you're doing :)
>
> same(?). The version is 4.0.5 ...it was fine before... yes ran it just now
>> for fws tuto... how long it takes time in your machine?
>>
>
> I have the same version.  The commands you showed completed in just a
> fraction of a second, like most simple solvation procedures.
>
> -Justin
>
>
>> On Sun, Oct 11, 2009 at 1:33 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Jamie Seyed wrote:
>>
>>Hi Justin,
>>yes resize.gro is a created file from editconf which has box
>>size of  5.05918 on the last line
>>my command was "editconf -bt cubic -f spc216.pdb -o resize.gro -d
>> 1"
>>
>>
>>Do you actually have separate spc216.pdb and spc216.gro files?  Just
>>trying to make sure this actually worked.
>>
>>
>>and for second command I changed 1 to 5 but it still stops in
>>the same point. I am trying to examine 2 methods that you & Mark
>>suggested me to
>>
>>
>>Very weird.  Both of your commands worked on my machine.  What
>>version of Gromacs are you using?  Does genbox work for other systems?
>>
>>-Justin
>>
>>create a box of water.../Many Thanks/Jamie
>>
>>On Sun, Oct 11, 2009 at 12:54 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>>>> wrote:
>>
>>
>>
>>   Jamie Seyed wrote:
>>
>>Dear Gmx users,
>>   Does any one know why genbox stops when I use this command:
>>   "genbox -cp resize.gro -cs spc216.gro -o b4em.pdb -p
>>topol.top"
>>   or when I use this command:
>>   "genbox -cs spc216.gro -box 1 1 1 -maxsol 500 -o out.gro -p
>>   topol.top"
>>   It goes until
>>   Reading solvent configuration
>>   Solvent configuration contains 648 atoms in 216 residues
>>   and then stops
>>   Would you please let me know why it happens?? Many Thanks in
>>   Advance/Jamie
>>
>>
>>   Is "resize.gro" a new file?  Or something you have created
>> before
>>   (i.e., an empty file with a box size defined)?
>>
>>   Defining -box 1 1 1 generates a 1-nm cubic box, which is almost
>>   certainly too small to contain 500 solvent molecules.  Define an
>>   appropriate box size.
>>
>>   -Justin
>>
>>
>>On Sun, Oct 11, 2009 at 12:04 PM, Jamie Seyed
>>   mailto:jamie.se...@gmail.com>
>>>
>>   > >>
>>   wrote:
>>
>>  Thanks to Justin & Mark for answering my second
>>question...
>>  Could any one give me a hint on my first question that
>>I copy
>>   it again?
>>  --about g_velacc and calculating the diffusion
>>constant from
>>   that.
>>  In mailing list people say that we need to divide it
>>by mass
>>   squared
>>  and 1/3. Then I found another recent post that said it
>>has been
>>  included in the code... Would you please clarify this
>>that if
>>   I need
>>  the factors or not. Also I found 2 numbers after
>>integration.
>>
>>  Integral   1   0.01595
>>  setaverage
>>  SS1   3.718082e-04
>>  Would you please inform me what are these number and
>>what is the
>>  relation between them?
>>  Many Thanks in Advance/Jamie
>>
>>  On Sat, Oct 10, 2009 at 8:39 PM, Justin A. Lemkul
>>   mailto:jalem...@vt.edu>
>>>
>>  
>>>
>>
>>
>>  Jamie Seyed wrote:
>>
>>  Dear Gmx Users,
>>  I have a 2 questions. First about g_velacc and
>>   calculating
>>  the diffusion constant from that. In mailing list
>>   people say
>>  that we need to divide it by mass squared and
>>1/3. Then

Re: [gmx-users] velacc & box of water

[Justin A. Lemkul]

Jamie Seyed wrote:
I converted  spc216.pdb to gro using editconf. SO they must be the 


I suppose that's fine, I just don't see all the need for interconverting file 
formats.  It just opens up the possibility of more errors if you don't keep 
track of what you're doing :)


same(?). The version is 4.0.5 ...it was fine before... yes ran it just 
now for fws tuto... how long it takes time in your machine?


I have the same version.  The commands you showed completed in just a fraction 
of a second, like most simple solvation procedures.


-Justin



On Sun, Oct 11, 2009 at 1:33 PM, Justin A. Lemkul > wrote:




Jamie Seyed wrote:

Hi Justin,
yes resize.gro is a created file from editconf which has box
size of  5.05918 on the last line
my command was "editconf -bt cubic -f spc216.pdb -o resize.gro -d 1"


Do you actually have separate spc216.pdb and spc216.gro files?  Just
trying to make sure this actually worked.


and for second command I changed 1 to 5 but it still stops in
the same point. I am trying to examine 2 methods that you & Mark
suggested me to


Very weird.  Both of your commands worked on my machine.  What
version of Gromacs are you using?  Does genbox work for other systems?

-Justin

create a box of water.../Many Thanks/Jamie

On Sun, Oct 11, 2009 at 12:54 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   Jamie Seyed wrote:

   Dear Gmx users,
   Does any one know why genbox stops when I use this command:
   "genbox -cp resize.gro -cs spc216.gro -o b4em.pdb -p
topol.top"
   or when I use this command:
   "genbox -cs spc216.gro -box 1 1 1 -maxsol 500 -o out.gro -p
   topol.top"
   It goes until
   Reading solvent configuration
   Solvent configuration contains 648 atoms in 216 residues
   and then stops
   Would you please let me know why it happens?? Many Thanks in
   Advance/Jamie


   Is "resize.gro" a new file?  Or something you have created before
   (i.e., an empty file with a box size defined)?

   Defining -box 1 1 1 generates a 1-nm cubic box, which is almost
   certainly too small to contain 500 solvent molecules.  Define an
   appropriate box size.

   -Justin


On Sun, Oct 11, 2009 at 12:04 PM, Jamie Seyed
   mailto:jamie.se...@gmail.com>
>
    
>
  

Re: [gmx-users] velacc & box of water

[Jamie Seyed]

I converted  spc216.pdb to gro using editconf. SO they must be the same(?).
The version is 4.0.5 ...it was fine before... yes ran it just now for fws
tuto... how long it takes time in your machine?

On Sun, Oct 11, 2009 at 1:33 PM, Justin A. Lemkul  wrote:

>
>
> Jamie Seyed wrote:
>
>> Hi Justin,
>> yes resize.gro is a created file from editconf which has box size of
>>  5.05918 on the last line
>> my command was "editconf -bt cubic -f spc216.pdb -o resize.gro -d 1"
>>
>
> Do you actually have separate spc216.pdb and spc216.gro files?  Just trying
> to make sure this actually worked.
>
> and for second command I changed 1 to 5 but it still stops in the same
>> point. I am trying to examine 2 methods that you & Mark suggested me to
>>
>
> Very weird.  Both of your commands worked on my machine.  What version of
> Gromacs are you using?  Does genbox work for other systems?
>
> -Justin
>
>  create a box of water.../Many Thanks/Jamie
>>
>> On Sun, Oct 11, 2009 at 12:54 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Jamie Seyed wrote:
>>
>>Dear Gmx users,
>>Does any one know why genbox stops when I use this command:
>>"genbox -cp resize.gro -cs spc216.gro -o b4em.pdb -p topol.top"
>>or when I use this command:
>>"genbox -cs spc216.gro -box 1 1 1 -maxsol 500 -o out.gro -p
>>topol.top"
>>It goes until
>>Reading solvent configuration
>>Solvent configuration contains 648 atoms in 216 residues
>>and then stops
>>Would you please let me know why it happens?? Many Thanks in
>>Advance/Jamie
>>
>>
>>Is "resize.gro" a new file?  Or something you have created before
>>(i.e., an empty file with a box size defined)?
>>
>>Defining -box 1 1 1 generates a 1-nm cubic box, which is almost
>>certainly too small to contain 500 solvent molecules.  Define an
>>appropriate box size.
>>
>>-Justin
>>
>>
>> On Sun, Oct 11, 2009 at 12:04 PM, Jamie Seyed
>>mailto:jamie.se...@gmail.com>
>>>>
>>wrote:
>>
>>   Thanks to Justin & Mark for answering my second question...
>>   Could any one give me a hint on my first question that I copy
>>it again?
>>   --about g_velacc and calculating the diffusion constant from
>>that.
>>   In mailing list people say that we need to divide it by mass
>>squared
>>   and 1/3. Then I found another recent post that said it has been
>>   included in the code... Would you please clarify this that if
>>I need
>>   the factors or not. Also I found 2 numbers after integration.
>>
>>   Integral   1   0.01595
>>   setaverage
>>   SS1   3.718082e-04
>>   Would you please inform me what are these number and what is the
>>   relation between them?
>>   Many Thanks in Advance/Jamie
>>
>>   On Sat, Oct 10, 2009 at 8:39 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>>>> wrote:
>>
>>
>>
>>   Jamie Seyed wrote:
>>
>>   Dear Gmx Users,
>>   I have a 2 questions. First about g_velacc and
>>calculating
>>   the diffusion constant from that. In mailing list
>>people say
>>   that we need to divide it by mass squared and 1/3. Then
>> I
>>   found another recent post that said it has been
>>included in
>>   the code... Would you please clarify this that if I
>>need the
>>   factors or not. Also I found 2 numbers after
>> integration.
>>   Integral   1   0.01595
>>   setaverage
>>   SS1   3.718082e-04
>>   --1) Would you please inform me what are these number
>> and
>>   what is the relation between them?
>>
>>   Can't comment on the first part...maybe the code will
>>point you
>>   in the right direction?
>>
>>
>>   --2) My second question is I want to make a box of only
>>   water (spce) with let say 500 water molecules. Would you
>>   please give me quick hints how to do it (the proper
>>way) or
>>   refer me to good point? Up to now I can only have 216
>>water
>>   molecules from tuto/water folder and I tried a lot
>>
>>
>>   This task might be approached in a couple of ways:
>>
>>   1. genconf -nbox to define a suitable number of replicate
>>systems.
>>   2. genbox -box -maxsol 500 to define a suitably-sized box
>> and
>>   fill it with only the desired number of molecules.
>>
>>   -Justin
>>
>>   to start from the beginning, but I could not ma

Re: [gmx-users] velacc & box of water

[Justin A. Lemkul]

Jamie Seyed wrote:

Hi Justin,
yes resize.gro is a created file from editconf which has box size of 
 5.05918 on the last line

my command was "editconf -bt cubic -f spc216.pdb -o resize.gro -d 1"


Do you actually have separate spc216.pdb and spc216.gro files?  Just trying to 
make sure this actually worked.


and for second command I changed 1 to 5 but it still stops in the same 
point. I am trying to examine 2 methods that you & Mark suggested me to 


Very weird.  Both of your commands worked on my machine.  What version of 
Gromacs are you using?  Does genbox work for other systems?


-Justin


create a box of water.../Many Thanks/Jamie

On Sun, Oct 11, 2009 at 12:54 PM, Justin A. Lemkul > wrote:




Jamie Seyed wrote:

Dear Gmx users,
Does any one know why genbox stops when I use this command:
"genbox -cp resize.gro -cs spc216.gro -o b4em.pdb -p topol.top"
or when I use this command:
"genbox -cs spc216.gro -box 1 1 1 -maxsol 500 -o out.gro -p
topol.top"
It goes until
Reading solvent configuration
Solvent configuration contains 648 atoms in 216 residues
and then stops
Would you please let me know why it happens?? Many Thanks in
Advance/Jamie


Is "resize.gro" a new file?  Or something you have created before
(i.e., an empty file with a box size defined)?

Defining -box 1 1 1 generates a 1-nm cubic box, which is almost
certainly too small to contain 500 solvent molecules.  Define an
appropriate box size.

-Justin


 On Sun, Oct 11, 2009 at 12:04 PM, Jamie Seyed
mailto:jamie.se...@gmail.com>
>>
wrote:

   Thanks to Justin & Mark for answering my second question...
   Could any one give me a hint on my first question that I copy
it again?
   --about g_velacc and calculating the diffusion constant from
that.
   In mailing list people say that we need to divide it by mass
squared
   and 1/3. Then I found another recent post that said it has been
   included in the code... Would you please clarify this that if
I need
   the factors or not. Also I found 2 numbers after integration.

   Integral   1   0.01595
   setaverage
   SS1   3.718082e-04
   Would you please inform me what are these number and what is the
   relation between them?
   Many Thanks in Advance/Jamie

   On Sat, Oct 10, 2009 at 8:39 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
   >> wrote:



   Jamie Seyed wrote:

   Dear Gmx Users,
   I have a 2 questions. First about g_velacc and
calculating
   the diffusion constant from that. In mailing list
people say
   that we need to divide it by mass squared and 1/3. Then I
   found another recent post that said it has been
included in
   the code... Would you please clarify this that if I
need the
   factors or not. Also I found 2 numbers after integration.
   Integral   1   0.01595
   setaverage
   SS1   3.718082e-04
   --1) Would you please inform me what are these number and
   what is the relation between them?
   


   Can't comment on the first part...maybe the code will
point you
   in the right direction?


   --2) My second question is I want to make a box of only
   water (spce) with let say 500 water molecules. Would you
   please give me quick hints how to do it (the proper
way) or
   refer me to good point? Up to now I can only have 216
water
   molecules from tuto/water folder and I tried a lot


   This task might be approached in a couple of ways:

   1. genconf -nbox to define a suitable number of replicate
systems.
   2. genbox -box -maxsol 500 to define a suitably-sized box and
   fill it with only the desired number of molecules.

   -Justin

   to start from the beginning, but I could not make it... I
   appreciate if you help me to understand the first
issue and
   be able to overcome the second one. Many Thanks in
Advance/Jamie


 
 




   ___
   gmx-users mailing listgmx-users@gromacs.org

 

Re: [gmx-users] velacc & box of water

[Jamie Seyed]

Hi Justin,
yes resize.gro is a created file from editconf which has box size of
 5.05918 on the last line
my command was "editconf -bt cubic -f spc216.pdb -o resize.gro -d 1"
and for second command I changed 1 to 5 but it still stops in the same
point. I am trying to examine 2 methods that you & Mark suggested me to
create a box of water.../Many Thanks/Jamie

On Sun, Oct 11, 2009 at 12:54 PM, Justin A. Lemkul  wrote:

>
>
> Jamie Seyed wrote:
>
>> Dear Gmx users,
>> Does any one know why genbox stops when I use this command:
>> "genbox -cp resize.gro -cs spc216.gro -o b4em.pdb -p topol.top"
>> or when I use this command:
>> "genbox -cs spc216.gro -box 1 1 1 -maxsol 500 -o out.gro -p topol.top"
>> It goes until
>> Reading solvent configuration
>> Solvent configuration contains 648 atoms in 216 residues
>> and then stops
>> Would you please let me know why it happens?? Many Thanks in Advance/Jamie
>>
>>
> Is "resize.gro" a new file?  Or something you have created before (i.e., an
> empty file with a box size defined)?
>
> Defining -box 1 1 1 generates a 1-nm cubic box, which is almost certainly
> too small to contain 500 solvent molecules.  Define an appropriate box size.
>
> -Justin
>
>
>>  On Sun, Oct 11, 2009 at 12:04 PM, Jamie Seyed > jamie.se...@gmail.com>> wrote:
>>
>>Thanks to Justin & Mark for answering my second question...
>>Could any one give me a hint on my first question that I copy it again?
>>--about g_velacc and calculating the diffusion constant from that.
>>In mailing list people say that we need to divide it by mass squared
>>and 1/3. Then I found another recent post that said it has been
>>included in the code... Would you please clarify this that if I need
>>the factors or not. Also I found 2 numbers after integration.
>>
>>Integral   1   0.01595
>>setaverage
>>SS1   3.718082e-04
>>Would you please inform me what are these number and what is the
>>relation between them?
>>Many Thanks in Advance/Jamie
>>
>>On Sat, Oct 10, 2009 at 8:39 PM, Justin A. Lemkul > > wrote:
>>
>>
>>
>>Jamie Seyed wrote:
>>
>>Dear Gmx Users,
>>I have a 2 questions. First about g_velacc and calculating
>>the diffusion constant from that. In mailing list people say
>>that we need to divide it by mass squared and 1/3. Then I
>>found another recent post that said it has been included in
>>the code... Would you please clarify this that if I need the
>>factors or not. Also I found 2 numbers after integration.
>>Integral   1   0.01595
>>setaverage
>>SS1   3.718082e-04
>>--1) Would you please inform me what are these number and
>>what is the relation between them?
>>
>>
>>Can't comment on the first part...maybe the code will point you
>>in the right direction?
>>
>>
>>--2) My second question is I want to make a box of only
>>water (spce) with let say 500 water molecules. Would you
>>please give me quick hints how to do it (the proper way) or
>>refer me to good point? Up to now I can only have 216 water
>>molecules from tuto/water folder and I tried a lot
>>
>>
>>This task might be approached in a couple of ways:
>>
>>1. genconf -nbox to define a suitable number of replicate systems.
>>2. genbox -box -maxsol 500 to define a suitably-sized box and
>>fill it with only the desired number of molecules.
>>
>>-Justin
>>
>>to start from the beginning, but I could not make it... I
>>appreciate if you help me to understand the first issue and
>>be able to overcome the second one. Many Thanks in
>> Advance/Jamie
>>
>>
>>
>>  
>>
>>
>>
>>___
>>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
>>
>>===

Re: [gmx-users] velacc & box of water

[Justin A. Lemkul]

Jamie Seyed wrote:

Dear Gmx users,
Does any one know why genbox stops when I use this command:
"genbox -cp resize.gro -cs spc216.gro -o b4em.pdb -p topol.top"
or when I use this command:
"genbox -cs spc216.gro -box 1 1 1 -maxsol 500 -o out.gro -p topol.top"
It goes until
Reading solvent configuration
Solvent configuration contains 648 atoms in 216 residues
and then stops
Would you please let me know why it happens?? Many Thanks in Advance/Jamie



Is "resize.gro" a new file?  Or something you have created before (i.e., an 
empty file with a box size defined)?


Defining -box 1 1 1 generates a 1-nm cubic box, which is almost certainly too 
small to contain 500 solvent molecules.  Define an appropriate box size.


-Justin



 
On Sun, Oct 11, 2009 at 12:04 PM, Jamie Seyed > wrote:


Thanks to Justin & Mark for answering my second question...
Could any one give me a hint on my first question that I copy it again?
--about g_velacc and calculating the diffusion constant from that.
In mailing list people say that we need to divide it by mass squared
and 1/3. Then I found another recent post that said it has been
included in the code... Would you please clarify this that if I need
the factors or not. Also I found 2 numbers after integration.

Integral   1   0.01595
setaverage
SS1   3.718082e-04
Would you please inform me what are these number and what is the
relation between them?
Many Thanks in Advance/Jamie

On Sat, Oct 10, 2009 at 8:39 PM, Justin A. Lemkul mailto:jalem...@vt.edu>> wrote:



Jamie Seyed wrote:

Dear Gmx Users,
I have a 2 questions. First about g_velacc and calculating
the diffusion constant from that. In mailing list people say
that we need to divide it by mass squared and 1/3. Then I
found another recent post that said it has been included in
the code... Would you please clarify this that if I need the
factors or not. Also I found 2 numbers after integration.
Integral   1   0.01595
setaverage
SS1   3.718082e-04
--1) Would you please inform me what are these number and
what is the relation between them?
 



Can't comment on the first part...maybe the code will point you
in the right direction?


--2) My second question is I want to make a box of only
water (spce) with let say 500 water molecules. Would you
please give me quick hints how to do it (the proper way) or
refer me to good point? Up to now I can only have 216 water
molecules from tuto/water folder and I tried a lot


This task might be approached in a couple of ways:

1. genconf -nbox to define a suitable number of replicate systems.
2. genbox -box -maxsol 500 to define a suitably-sized box and
fill it with only the desired number of molecules.

-Justin

to start from the beginning, but I could not make it... I
appreciate if you help me to understand the first issue and
be able to overcome the second one. Many Thanks in Advance/Jamie







___
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




---

Re: [gmx-users] velacc & box of water

[Jamie Seyed]

Dear Gmx users,
Does any one know why genbox stops when I use this command:
"genbox -cp resize.gro -cs spc216.gro -o b4em.pdb -p topol.top"
or when I use this command:
"genbox -cs spc216.gro -box 1 1 1 -maxsol 500 -o out.gro -p topol.top"
It goes until
Reading solvent configuration
Solvent configuration contains 648 atoms in 216 residues
and then stops
Would you please let me know why it happens?? Many Thanks in Advance/Jamie



On Sun, Oct 11, 2009 at 12:04 PM, Jamie Seyed  wrote:

> Thanks to Justin & Mark for answering my second question...
> Could any one give me a hint on my first question that I copy it again?
> --about g_velacc and calculating the diffusion constant from that. In
> mailing list people say that we need to divide it by mass squared and 1/3.
> Then I found another recent post that said it has been included in the
> code... Would you please clarify this that if I need the factors or not.
> Also I found 2 numbers after integration.
> Integral   1   0.01595
> setaverage
> SS1   3.718082e-04
> Would you please inform me what are these number and what is the relation
> between them?
> Many Thanks in Advance/Jamie
>
>   On Sat, Oct 10, 2009 at 8:39 PM, Justin A. Lemkul wrote:
>
>>
>>
>> Jamie Seyed wrote:
>>
>>> Dear Gmx Users,
>>> I have a 2 questions. First about g_velacc and calculating the diffusion
>>> constant from that. In mailing list people say that we need to divide it by
>>> mass squared and 1/3. Then I found another recent post that said it has been
>>> included in the code... Would you please clarify this that if I need the
>>> factors or not. Also I found 2 numbers after integration.
>>> Integral   1   0.01595
>>> setaverage
>>> SS1   3.718082e-04
>>> --1) Would you please inform me what are these number and what is the
>>> relation between them?
>>>
>>>
>>
>> Can't comment on the first part...maybe the code will point you in the
>> right direction?
>>
>> --2) My second question is I want to make a box of only water (spce) with
>>> let say 500 water molecules. Would you please give me quick hints how to do
>>> it (the proper way) or refer me to good point? Up to now I can only have 216
>>> water molecules from tuto/water folder and I tried a lot
>>>
>>
>> This task might be approached in a couple of ways:
>>
>> 1. genconf -nbox to define a suitable number of replicate systems.
>> 2. genbox -box -maxsol 500 to define a suitably-sized box and fill it with
>> only the desired number of molecules.
>>
>> -Justin
>>
>>  to start from the beginning, but I could not make it... I appreciate if
>>> you help me to understand the first issue and be able to overcome the second
>>> one. Many Thanks in Advance/Jamie
>>>
>>>
>>> 
>>>
>>> ___
>>> 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
>>
>
>
___
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

Re: [gmx-users] velacc & box of water

[Jamie Seyed]

Thanks to Justin & Mark for answering my second question...
Could any one give me a hint on my first question that I copy it again?
--about g_velacc and calculating the diffusion constant from that. In
mailing list people say that we need to divide it by mass squared and 1/3.
Then I found another recent post that said it has been included in the
code... Would you please clarify this that if I need the factors or not.
Also I found 2 numbers after integration.
Integral   1   0.01595
setaverage
SS1   3.718082e-04
Would you please inform me what are these number and what is the relation
between them?
Many Thanks in Advance/Jamie

On Sat, Oct 10, 2009 at 8:39 PM, Justin A. Lemkul  wrote:

>
>
> Jamie Seyed wrote:
>
>> Dear Gmx Users,
>> I have a 2 questions. First about g_velacc and calculating the diffusion
>> constant from that. In mailing list people say that we need to divide it by
>> mass squared and 1/3. Then I found another recent post that said it has been
>> included in the code... Would you please clarify this that if I need the
>> factors or not. Also I found 2 numbers after integration.
>> Integral   1   0.01595
>> setaverage
>> SS1   3.718082e-04
>> --1) Would you please inform me what are these number and what is the
>> relation between them?
>>
>>
>
> Can't comment on the first part...maybe the code will point you in the
> right direction?
>
> --2) My second question is I want to make a box of only water (spce) with
>> let say 500 water molecules. Would you please give me quick hints how to do
>> it (the proper way) or refer me to good point? Up to now I can only have 216
>> water molecules from tuto/water folder and I tried a lot
>>
>
> This task might be approached in a couple of ways:
>
> 1. genconf -nbox to define a suitable number of replicate systems.
> 2. genbox -box -maxsol 500 to define a suitably-sized box and fill it with
> only the desired number of molecules.
>
> -Justin
>
>  to start from the beginning, but I could not make it... I appreciate if
>> you help me to understand the first issue and be able to overcome the second
>> one. Many Thanks in Advance/Jamie
>>
>>
>> 
>>
>> ___
>> 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
>
___
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

Re: [gmx-users] velacc & box of water

[Justin A. Lemkul]

Jamie Seyed wrote:

Dear Gmx Users,
I have a 2 questions. First about g_velacc and calculating the diffusion 
constant from that. In mailing list people say that we need to divide it 
by mass squared and 1/3. Then I found another recent post that said it 
has been included in the code... Would you please clarify this that if I 
need the factors or not. Also I found 2 numbers after integration.

Integral   1   0.01595
setaverage
SS1   3.718082e-04
--1) Would you please inform me what are these number and what is the 
relation between them?
 


Can't comment on the first part...maybe the code will point you in the right 
direction?


--2) My second question is I want to make a box of only water (spce) 
with let say 500 water molecules. Would you please give me quick hints 
how to do it (the proper way) or refer me to good point? Up to now I can 
only have 216 water molecules from tuto/water folder and I tried a lot 


This task might be approached in a couple of ways:

1. genconf -nbox to define a suitable number of replicate systems.
2. genbox -box -maxsol 500 to define a suitably-sized box and fill it with only 
the desired number of molecules.


-Justin

to start from the beginning, but I could not make it... I appreciate if 
you help me to understand the first issue and be able to overcome the 
second one. Many Thanks in Advance/Jamie





___
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

Re: [gmx-users] velacc & box of water

[Mark Abraham]

Jamie Seyed wrote:

Dear Gmx Users,
I have a 2 questions. First about g_velacc and calculating the diffusion 
constant from that. In mailing list people say that we need to divide it 
by mass squared and 1/3. Then I found another recent post that said it 
has been included in the code... Would you please clarify this that if I 
need the factors or not. Also I found 2 numbers after integration.

Integral   1   0.01595
setaverage
SS1   3.718082e-04
--1) Would you please inform me what are these number and what is the 
relation between them?
 
--2) My second question is I want to make a box of only water (spce) 
with let say 500 water molecules. Would you please give me quick hints 
how to do it (the proper way) or refer me to good point? Up to now I can 
only have 216 water molecules from tuto/water folder and I tried a lot 
to start from the beginning, but I could not make it... I appreciate if 
you help me to understand the first issue and be able to overcome the 
second one. Many Thanks in Advance/Jamie


genconf will allow you to stack multiples of that 216 box. Or, use 
editconf to adjust the size of a 216 box, and genbox to fill it to get a 
number that suits your fancy. In either case you will need to 
equilibrate before trying to measure velacc, just as with any other 
observable.


Mark
___
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

[gmx-users] velacc & box of water

[Jamie Seyed]

Dear Gmx Users,
I have a 2 questions. First about g_velacc and calculating the diffusion
constant from that. In mailing list people say that we need to divide it by
mass squared and 1/3. Then I found another recent post that said it has been
included in the code... Would you please clarify this that if I need the
factors or not. Also I found 2 numbers after integration.
Integral   1   0.01595
setaverage
SS1   3.718082e-04
--1) Would you please inform me what are these number and what is the
relation between them?

--2) My second question is I want to make a box of only water (spce) with
let say 500 water molecules. Would you please give me quick hints how to do
it (the proper way) or refer me to good point? Up to now I can only have 216
water molecules from tuto/water folder and I tried a lot to start from the
beginning, but I could not make it... I appreciate if you help me to
understand the first issue and be able to overcome the second one. Many
Thanks in Advance/Jamie
___
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