[gmx-users] Re: g_velacc

[Vitaly Chaban]

>
> Hello,
>
> I have calculated the velocity autocorrelation function of OH bond
> in glucose molecule. For this calculation I modified the index file. The
> modified part is pasted below.
>
> [ O10 ]
>  10   20
>
> 10 is oxygen no. and 20 is oxygen.
>
> I used following command to calculate the velocity autocorrelation function.
>
>  g_velacc -f 6.trr -s 6.tpr  -n index.ndx -e 100 -nonormalize  -o
>
>
> My question is how does the prog. calculate the velocity autocorrlation
> function.
>
> Does is subtract the velocity of hydrogen from oxygen and then calculate
> the autocorrelation function?



The program acts as if your hydrogen and oxygen are identical atoms.


-- 
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216
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Re:Re: [gmx-users] what's the philosophy of -ci option in "genbox"?

[Jinan Niu]

Lemkul, thanks
At 2011-05-25 18:56:59，"Justin A. Lemkul"  wrote:
>
>
>牛继南 wrote:
>> Hi，gmx users:
>> Recently, I have a question——what's the philosophy of -ci option in 
>> "genbox"?
>> My understanding is that a molecule is randomly generated in the hole at 
>> first, then a new location around the molecule is generated according 
>> to  a random seed , then gmx checks whether solve 
>> or solute molecules will overlap, and so on. What is correct?
>> 
>
>A random location is generated, and the position is accepted if there is no 
>overlap with nearby molecules.  See the insert_mols() function in gmx_genbox.c.
>
>-Justin
>
>> --
>> Sincerely yours 
>> Dr Ji-Nan Niu 
>> School of Materials Science and Engineering.
>> China University of Mining and Technology.
>> Jiangsu Province, XuZhou 221116
>> P. R. China
>> _
>> Email: njn0...@cumt.edu.cn  Phone: 
>> +86-13852039305
>> 
>> 
>> 
>
>-- 
>
>
>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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[gmx-users] Error while trying REMD on cluster

[vivek sharma]

HI GMX-users,
 I am trying to run a REMD simulation on my system. I have created 10 .tpr
files and fired the simulation using the following command
-
bsub -n 40 -o out_1 -e err_1 mpirun mdrun_d -s MD.tpr -multi 10 -replex 2 -o
MD.trr -e MD.edr -g MD.log -c MD.gro &
---
\
 I am firing this run on a cluster. after firing the command teh simulation
is crashing with following error reported in err_1 file.
-
Program mdrun_d, VERSION 4.5.4
Source code file: main.c, line: 420

Fatal error:
The number of nodes (1) is not a multiple of the number of simulations (10)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
--

Can anybody comment or suggest the reason for such error.

regards,
Vivek
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Re: [gmx-users] Re: g_velacc

[Nilesh Dhumal]

20 is hydrogen atom.
Sorry its typing mistake.

Nilesh

On Fri, May 27, 2011 3:52 am, Vitaly Chaban wrote:
>>

>> Hello,
>>
>>
>> I have calculated the velocity autocorrelation function of OH bond
>> in glucose molecule. For this calculation I modified the index file. The
>>  modified part is pasted below.
>>
>> [ O10 ]
>>  10   20
>>
>>
>> 10 is oxygen no. and 20 is oxygen.
>>
>>
>> I used following command to calculate the velocity autocorrelation
>> function.
>>
>>  g_velacc -f 6.trr -s 6.tpr  -n index.ndx -e 100 -nonormalize  -o
>>
>>
>>
>> My question is how does the prog. calculate the velocity autocorrlation
>>  function.
>>
>> Does is subtract the velocity of hydrogen from oxygen and then
>> calculate the autocorrelation function?
>
>
>
> The program acts as if your hydrogen and oxygen are identical atoms.
>
>
>
> --
> Dr. Vitaly V. Chaban, Department of Chemistry
> University of Rochester, Rochester, New York 14627-0216
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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> http://www.gromacs.org/Support/Mailing_Lists
>
>
>


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Re: [gmx-users] Error while trying REMD on cluster

[Justin A. Lemkul]

vivek sharma wrote:

HI GMX-users,
 I am trying to run a REMD simulation on my system. I have created 10 
.tpr files and fired the simulation using the following command

-
bsub -n 40 -o out_1 -e err_1 mpirun mdrun_d -s MD.tpr -multi 10 -replex 
2 -o MD.trr -e MD.edr -g MD.log -c MD.gro &

---
\
 I am firing this run on a cluster. after firing the command teh 
simulation is crashing with following error reported in err_1 file.

-
Program mdrun_d, VERSION 4.5.4
Source code file: main.c, line: 420

Fatal error:
The number of nodes (1) is not a multiple of the number of simulations (10)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
--

Can anybody comment or suggest the reason for such error.



You're only running on one processor.  You probably need "mpirun -np 40" rather 
than just "mpirun" in the command.


-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] Re: g_velacc

[Vitaly Chaban]

It does not change the situation, I believe.

What is the sense of calculating such ACF? In order to understand the
cross-correlation between the bonded atoms? It will be huge as I
understand.


-- 
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216




On Fri, May 27, 2011 at 8:07 AM, Nilesh Dhumal  wrote:
> 20 is hydrogen atom.
> Sorry its typing mistake.
>
> Nilesh
>
> On Fri, May 27, 2011 3:52 am, Vitaly Chaban wrote:
>>>
>
>>> Hello,
>>>
>>>
>>> I have calculated the velocity autocorrelation function of OH bond
>>> in glucose molecule. For this calculation I modified the index file. The
>>>  modified part is pasted below.
>>>
>>> [ O10 ]
>>>  10   20
>>>
>>>
>>> 10 is oxygen no. and 20 is oxygen.
>>>
>>>
>>> I used following command to calculate the velocity autocorrelation
>>> function.
>>>
>>>  g_velacc -f 6.trr -s 6.tpr  -n index.ndx -e 100 -nonormalize  -o
>>>
>>>
>>>
>>> My question is how does the prog. calculate the velocity autocorrlation
>>>  function.
>>>
>>> Does is subtract the velocity of hydrogen from oxygen and then
>>> calculate the autocorrelation function?
>>
>>
>>
>> The program acts as if your hydrogen and oxygen are identical atoms.
>>
>>
>>
>> --
>> Dr. Vitaly V. Chaban, Department of Chemistry
>> University of Rochester, Rochester, New York 14627-0216
>> --
>> gmx-users mailing list    gmx-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!
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>> http://www.gromacs.org/Support/Mailing_Lis
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Re: [gmx-users] g_velacc

[Nilesh Dhumal]

I am  calculating OH stretching frequency by fourier transform of velocity
autocorrelation function.

I could calculate the OH stretching frequnecy by calculating fourier
transform of OH bond.

I want to know how gromacs calculate the velocity autocorrelation function
of a bond (If I define a bond in index file).

Does is subtract the velocity of hydrogen from oxygen and then
calculate the autocorrelation function?

Nilesh




On Fri, May 27, 2011 2:37 am, David van der Spoel wrote:
> On 2011-05-26 22.48, Nilesh Dhumal wrote:
>
>> Hello,
>>
>>
>> I have calculated the velocity autocorrelation function of OH bond
>> in glucose molecule. For this calculation I modified the index file. The
>>  modified part is pasted below.
>>
>> [ O10 ]
>> 10   20
>>
>
> where is the hydrogen? g_velacc knows nothing about bonds just atoms.
>
>>
>> 10 is oxygen no. and 20 is oxygen.
>>
>>
>> I used following command to calculate the velocity autocorrelation
>> function.
>>
>> g_velacc -f 6.trr -s 6.tpr  -n index.ndx -e 100 -nonormalize  -o
>>
>>
>> My question is how does the prog. calculate the velocity autocorrlation
>>  function.
>>
>> Does is subtract the velocity of hydrogen from oxygen and then
>> calculate the autocorrelation function?
>>
>> I am using gromacs version 4.0.7.
>>
>>
>> Thanks
>>
>>
>> Nilesh
>>
>>
>>
>>
>>
>>
>
>
> --
> 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 --
> 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
>
>
>


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Re: [gmx-users] g_velacc

[Justin A. Lemkul]

Nilesh Dhumal wrote:

I am  calculating OH stretching frequency by fourier transform of velocity
autocorrelation function.

I could calculate the OH stretching frequnecy by calculating fourier
transform of OH bond.

I want to know how gromacs calculate the velocity autocorrelation function
of a bond (If I define a bond in index file).

Does is subtract the velocity of hydrogen from oxygen and then
calculate the autocorrelation function?



See manual sections 8.5.3 and 8.5.4.  I doubt g_velacc does anything this 
complex.  Check the code to be sure, but based on the equation in 8.5.4, it 
would seem not.


-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] g_velacc

[David van der Spoel]

On 2011-05-27 14.26, Nilesh Dhumal wrote:

I am  calculating OH stretching frequency by fourier transform of velocity
autocorrelation function.

I could calculate the OH stretching frequnecy by calculating fourier
transform of OH bond.

I want to know how gromacs calculate the velocity autocorrelation function
of a bond (If I define a bond in index file).

Does is subtract the velocity of hydrogen from oxygen and then
calculate the autocorrelation function?

No, see below! There is no tool that does exactly what you want, however 
doing the velacc of just the hydrogen will come close.

Nilesh




On Fri, May 27, 2011 2:37 am, David van der Spoel wrote:

On 2011-05-26 22.48, Nilesh Dhumal wrote:


Hello,


I have calculated the velocity autocorrelation function of OH bond
in glucose molecule. For this calculation I modified the index file. The
  modified part is pasted below.

[ O10 ]
10   20



where is the hydrogen? g_velacc knows nothing about bonds just atoms.



10 is oxygen no. and 20 is oxygen.


I used following command to calculate the velocity autocorrelation
function.

g_velacc -f 6.trr -s 6.tpr  -n index.ndx -e 100 -nonormalize  -o


My question is how does the prog. calculate the velocity autocorrlation
  function.

Does is subtract the velocity of hydrogen from oxygen and then
calculate the autocorrelation function?

I am using gromacs version 4.0.7.


Thanks


Nilesh









--
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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--
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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Re: [gmx-users] Re: g_velacc

[Vitaly Chaban]

As I said before, g_velacc treats all the atoms in your index file as
if they were identical. It does NOT subtract anything.




On Fri, May 27, 2011 at 8:19 AM, Nilesh Dhumal  wrote:
> I am  calculating OH stretching frequency by fourier transform of velocity
> autocorrelation function.
>
> I could calculate the OH stretching frequnecy by calculating fourier
> transform of OH bond.
>
> I want to know how gromacs calculate the velocity autocorrelation function
> of a bond (If I define a bond in index file).
>
> Does is subtract the velocity of hydrogen from oxygen and then
> calculate the autocorrelation function?
>
> Nilesh
>
>
> On Fri, May 27, 2011 8:11 am, Vitaly Chaban wrote:
>> It does not change the situation, I believe.
>>
>>
>> What is the sense of calculating such ACF? In order to understand the
>> cross-correlation between the bonded atoms? It will be huge as I
>> understand.
>>
>>
>> --
>> Dr. Vitaly V. Chaban, Department of Chemistry
>> University of Rochester, Rochester, New York 14627-0216
>>
>>
>>
>>
>>
>> On Fri, May 27, 2011 at 8:07 AM, Nilesh Dhumal 
>> wrote:
>>
>>> 20 is hydrogen atom.
>>> Sorry its typing mistake.
>>>
>>>
>>> Nilesh
>>>
>>>
>>> On Fri, May 27, 2011 3:52 am, Vitaly Chaban wrote:
>>>
>
>>>
> Hello,
>
>
>
> I have calculated the velocity autocorrelation function of OH bond
> in glucose molecule. For this calculation I modified the index file.
> The
>  modified part is pasted below.
>
>
> [ O10 ]
>  10   20
>
>
>
> 10 is oxygen no. and 20 is oxygen.
>
>
>
> I used following command to calculate the velocity autocorrelation
> function.
>
>  g_velacc -f 6.trr -s 6.tpr  -n index.ndx -e 100 -nonormalize  -o
>
>
>
>
> My question is how does the prog. calculate the velocity
> autocorrlation  function.
>
>
> Does is subtract the velocity of hydrogen from oxygen and then
> calculate the autocorrelation function?



 The program acts as if your hydrogen and oxygen are identical atoms.




 --
 Dr. Vitaly V. Chaban, Department of Chemistry
 University of Rochester, Rochester, New York 14627-0216
 --
 gmx-users mailing list    gmx-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_Lis

>>
>>
>
>
>



-- 
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216
--
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Re: [gmx-users] Re: g_velacc

[Nilesh Dhumal]

How can I calculate the velocity autocorrelation function of a bond with
Gromacs?

Nilesh



On Fri, May 27, 2011 8:32 am, Vitaly Chaban wrote:
> As I said before, g_velacc treats all the atoms in your index file as
> if they were identical. It does NOT subtract anything.
>
>
>
>
> On Fri, May 27, 2011 at 8:19 AM, Nilesh Dhumal 
> wrote:
>
>> I am  calculating OH stretching frequency by fourier transform of
>> velocity autocorrelation function.
>>
>> I could calculate the OH stretching frequnecy by calculating fourier
>> transform of OH bond.
>>
>> I want to know how gromacs calculate the velocity autocorrelation
>> function of a bond (If I define a bond in index file).
>>
>> Does is subtract the velocity of hydrogen from oxygen and then
>> calculate the autocorrelation function?
>>
>> Nilesh
>>
>>
>>
>> On Fri, May 27, 2011 8:11 am, Vitaly Chaban wrote:
>>
>>> It does not change the situation, I believe.
>>>
>>>
>>>
>>> What is the sense of calculating such ACF? In order to understand the
>>>  cross-correlation between the bonded atoms? It will be huge as I
>>> understand.
>>>
>>>
>>> --
>>> Dr. Vitaly V. Chaban, Department of Chemistry
>>> University of Rochester, Rochester, New York 14627-0216
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Fri, May 27, 2011 at 8:07 AM, Nilesh Dhumal
>>> 
>>> wrote:
>>>
>>>
 20 is hydrogen atom.
 Sorry its typing mistake.



 Nilesh



 On Fri, May 27, 2011 3:52 am, Vitaly Chaban wrote:


>>

>> Hello,
>>
>>
>>
>>
>> I have calculated the velocity autocorrelation function of OH
>> bond in glucose molecule. For this calculation I modified the
>> index file. The
>>  modified part is pasted below.
>>
>>
>>
>> [ O10 ]
>>  10   20
>>
>>
>>
>>
>> 10 is oxygen no. and 20 is oxygen.
>>
>>
>>
>>
>> I used following command to calculate the velocity
>> autocorrelation function.
>>
>>  g_velacc -f 6.trr -s 6.tpr  -n index.ndx -e 100 -nonormalize
>>  -o
>>
>>
>>
>>
>>
>> My question is how does the prog. calculate the velocity
>> autocorrlation  function.
>>
>>
>> Does is subtract the velocity of hydrogen from oxygen and then
>> calculate the autocorrelation function?
>
>
>
> The program acts as if your hydrogen and oxygen are identical
> atoms.
>
>
>
>
> --
> Dr. Vitaly V. Chaban, Department of Chemistry
> University of Rochester, Rochester, New York 14627-0216
> --
> gmx-users mailing list    gmx-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_Lis
>
>
>>>
>>>
>>
>>
>>
>
>
>
> --
> Dr. Vitaly V. Chaban, Department of Chemistry
> University of Rochester, Rochester, New York 14627-0216
>
>
>


-- 
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Re: [gmx-users] g_velacc

[Nilesh Dhumal]

How can I calculate the velocity autocorrelation function of a bond with
Gromacs?

Nilesh



On Fri, May 27, 2011 8:31 am, David van der Spoel wrote:
> On 2011-05-27 14.26, Nilesh Dhumal wrote:
>
>> I am  calculating OH stretching frequency by fourier transform of
>> velocity autocorrelation function.
>>
>> I could calculate the OH stretching frequnecy by calculating fourier
>> transform of OH bond.
>>
>> I want to know how gromacs calculate the velocity autocorrelation
>> function of a bond (If I define a bond in index file).
>>
>> Does is subtract the velocity of hydrogen from oxygen and then
>> calculate the autocorrelation function?
>>
> No, see below! There is no tool that does exactly what you want, however
> doing the velacc of just the hydrogen will come close.
>> Nilesh
>>
>>
>>
>>
>>
>> On Fri, May 27, 2011 2:37 am, David van der Spoel wrote:
>>
>>> On 2011-05-26 22.48, Nilesh Dhumal wrote:
>>>
>>>
 Hello,



 I have calculated the velocity autocorrelation function of OH bond
 in glucose molecule. For this calculation I modified the index file.
 The
 modified part is pasted below.

 [ O10 ]
 10   20


>>>
>>> where is the hydrogen? g_velacc knows nothing about bonds just atoms.
>>>
>>>

 10 is oxygen no. and 20 is oxygen.



 I used following command to calculate the velocity autocorrelation
 function.

 g_velacc -f 6.trr -s 6.tpr  -n index.ndx -e 100 -nonormalize  -o


 My question is how does the prog. calculate the velocity
 autocorrlation function.

 Does is subtract the velocity of hydrogen from oxygen and then
 calculate the autocorrelation function?

 I am using gromacs version 4.0.7.



 Thanks



 Nilesh







>>>
>>>
>>> --
>>> 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 -- gmx-users mailing
>>> listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>> Read
>>> http://www.gromacs.org/Support/Mailing_Lists
>>>
>>>
>>>
>>>
>>
>>
>
>
> --
> 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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Re: [gmx-users] g_velacc

[David van der Spoel]

On 2011-05-27 14.39, Nilesh Dhumal wrote:

How can I calculate the velocity autocorrelation function of a bond with
Gromacs?


READ OUR ANSWERS.


Nilesh



On Fri, May 27, 2011 8:31 am, David van der Spoel wrote:

On 2011-05-27 14.26, Nilesh Dhumal wrote:


I am  calculating OH stretching frequency by fourier transform of
velocity autocorrelation function.

I could calculate the OH stretching frequnecy by calculating fourier
transform of OH bond.

I want to know how gromacs calculate the velocity autocorrelation
function of a bond (If I define a bond in index file).

Does is subtract the velocity of hydrogen from oxygen and then
calculate the autocorrelation function?


No, see below! There is no tool that does exactly what you want, however
doing the velacc of just the hydrogen will come close.

Nilesh





On Fri, May 27, 2011 2:37 am, David van der Spoel wrote:


On 2011-05-26 22.48, Nilesh Dhumal wrote:



Hello,



I have calculated the velocity autocorrelation function of OH bond
in glucose molecule. For this calculation I modified the index file.
The
modified part is pasted below.

[ O10 ]
10   20




where is the hydrogen? g_velacc knows nothing about bonds just atoms.




10 is oxygen no. and 20 is oxygen.



I used following command to calculate the velocity autocorrelation
function.

g_velacc -f 6.trr -s 6.tpr  -n index.ndx -e 100 -nonormalize  -o


My question is how does the prog. calculate the velocity
autocorrlation function.

Does is subtract the velocity of hydrogen from oxygen and then
calculate the autocorrelation function?

I am using gromacs version 4.0.7.



Thanks



Nilesh










--
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Dept. of Cell&   Molec. Biol., Uppsala University.
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
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[gmx-users] oplsaa vs. charmm

[simon sham]

Hi,
I have recently done two simulations on a protein at high temperature near its 
melting temperature. At the beginning I used CHARMM forcefield, and then OPLSAA 
to double check the results. There are some differences in the structures 
between the forcefield used.  I know different forcefields can give different 
results. All parameters in the simulations were the same except the forcefield. 
Is there anyway I can tell which forcefield gives more reliable results?

Thanks for the insights,

Simon
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Re: [gmx-users] oplsaa vs. charmm

[Justin A. Lemkul]

simon sham wrote:

Hi,
I have recently done two simulations on a protein at high temperature 
near its melting temperature. At the beginning I used CHARMM forcefield, 
and then OPLSAA to double check the results. There are some differences 
in the structures between the forcefield used.  I know different 
forcefields can give different results. All parameters in the 
simulations were the same except the forcefield. Is there anyway I can 
tell which forcefield gives more reliable results?


Compare with experimental results.  Without something to compare to, each is 
just a prediction of some unknown phenomenon.  Keep in mind that a single 
trajectory for either is not necessarily conclusive of anything.  Replicates and 
good sampling will be more informative.


-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] oplsaa vs. charmm

[David van der Spoel]

On 2011-05-27 17.50, simon sham wrote:

Hi,
I have recently done two simulations on a protein at high temperature
near its melting temperature. At the beginning I used CHARMM forcefield,
and then OPLSAA to double check the results. There are some differences
in the structures between the forcefield used. I know different
forcefields can give different results. All parameters in the
simulations were the same except the forcefield. Is there anyway I can
tell which forcefield gives more reliable results?

Thanks for the insights,

Simon


You might want to check

Oliver Lange, David van der Spoel and Bert de Groot: Scrutinizing 
Molecular Mechanics Force Fields on the Microsecond Timescale With NMR 
Data Biophys. J. 99 pp. 647-655 (2010)


where we compare a number of FFs to NMR data.

--
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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Re: [gmx-users] oplsaa vs. charmm

[Peter C. Lai]

On 2011-05-27 10:50:14AM -0500, simon sham wrote:
> Hi,
> I have recently done two simulations on a protein at high temperature near 
> its melting temperature. At the beginning I used CHARMM forcefield, and then 
> OPLSAA to double check the results. There are some differences in the 
> structures between the forcefield used.  I know different forcefields can 
> give different results. All parameters in the simulations were the same 
> except the forcefield. Is there anyway I can tell which forcefield gives more 
> reliable results?
> 

Also you never stated what RMSD/RMSFs between the two and if they are
significant to what you care to see (i.e. if you expect, say, alpha
helix to random coil transition, what changes in the unfolding do you see
that make you suspect one forcefield is better than the other?). Also if this 
is in a solvated system, the rest of the forcefield has been parameterized 
with the implicit assumption that TIPS3P (Charmm-specific) water will be used 
so make sure you have switched your water type when using CHARMM.

-- 
==
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | BEC 257
Genetics, Div. of Research  | 1150 10th Avenue South
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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[gmx-users] Schlitters entropy calculation

[Bala subramanian]

Friends,
I am a newbie to gromacs, trying to calculate the Schlitters entropy
calculation using the following commands.

g_covar -f  mytraj.xtc  -s  structure.pdb -n index.ndx -b 0 -e 4000 -mwa
-ref
g_anaeig -entropy  -temp 300

When i used the above commands, i get the Schlitter entropy value for the
4000 frames, but if i use less than 4000 frames, the program does not
calculate the entropy value and it shows the following result. This happens
irrespective of the region i select from the trajectory or the subset of
atoms i choose for the calculation. I am using gromacs version 4.5.3. I have
the same problem even with previous version of gromacs.

The Entropy due to the Quasi Harmonic approximation is 14895 J/mol K
The Entropy due to the Schlitter formula is nan J/mol K

Any suggestion on what could be going wront.
Bala
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Re: [gmx-users] Schlitters entropy calculation

[David van der Spoel]

On 2011-05-27 18.11, Bala subramanian wrote:

Friends,
I am a newbie to gromacs, trying to calculate the Schlitters entropy
calculation using the following commands.

g_covar -f  mytraj.xtc  -s  structure.pdb -n index.ndx -b 0 -e 4000 -mwa
-ref
g_anaeig -entropy  -temp 300

The formula contains many logarithms. Maybe one of them get zero as an 
argument. Please check the source code to debug this.




When i used the above commands, i get the Schlitter entropy value for
the 4000 frames, but if i use less than 4000 frames, the program does
not calculate the entropy value and it shows the following result. This
happens irrespective of the region i select from the trajectory or the
subset of atoms i choose for the calculation. I am using gromacs version
4.5.3. I have the same problem even with previous version of gromacs.

The Entropy due to the Quasi Harmonic approximation is 14895 J/mol K
The Entropy due to the Schlitter formula is nan J/mol K

Any suggestion on what could be going wront.
Bala




--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
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Re: [gmx-users] oplsaa vs. charmm

[simon sham]

Hi,
Once again, I appreciate all the responses.
1. To correct I just had in the previous email. I used GROMOS53ab not CHARMM. 
My apology.
2. At high temperaure, one of the helical turn in a alpha helix (3 residues) 
turns into a coil in GROMOS forcefield throughout the 20ns simulation. It was 
only slightly distorted in OPLSAA simulation in 20ns. 
3. The RMSF (backbone) for those 3 residues: 0.3nm in GROMOS vs. 0.1 nm in 
OPLSAA.

As I mentioned, the protein is near its melting temperature, therefore, I am 
not surprised to see some helix to coil transition or helical distortions. As 
Justin has suggested, I probably will try to make a longer run to see what will 
happen.

Best,

Simon
--- On Fri, 5/27/11, Peter C. Lai  wrote:

From: Peter C. Lai 
Subject: Re: [gmx-users] oplsaa vs. charmm
To: "simon sham" 
Cc: "gmx-users@gromacs.org" 
Date: Friday, May 27, 2011, 9:05 AM

On 2011-05-27 10:50:14AM -0500, simon sham wrote:
> Hi,
> I have recently done two simulations on a protein at high temperature near 
> its melting temperature. At the beginning I used CHARMM forcefield, and then 
> OPLSAA to double check the results. There are some differences in the 
> structures between the forcefield used.  I know different forcefields can 
> give different results. All parameters in the simulations were the same 
> except the forcefield. Is there anyway I can tell which forcefield gives more 
> reliable results?
> 

Also you never stated what RMSD/RMSFs between the two and if they are
significant to what you care to see (i.e. if you expect, say, alpha
helix to random coil transition, what changes in the unfolding do you see
that make you suspect one forcefield is better than the other?). Also if this 
is in a solvated system, the rest of the forcefield has been parameterized 
with the implicit assumption that TIPS3P (Charmm-specific) water will be used 
so make sure you have switched your water type when using CHARMM.

-- 
==
Peter C. Lai            | University of Alabama-Birmingham
Programmer/Analyst        | BEC 257
Genetics, Div. of Research    | 1150 10th Avenue South
p...@uab.edu            | Birmingham AL 35294-4461
(205) 690-0808            |
==

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[gmx-users] protein-ligand interaction

[ahmet yıldırım]

Dear users,

I want to investigate *Ligand effect *on the protein .
To investigation the interaction of protein-ligand:
*RMSD calculations:*
1.
a) RMSD of Backbone
b) RMSD of Backbone+ligand
2.
a) RMSD of Protein
b) RMSD of Protein+ligand
3.
a) RMSD of Protein-H
b) RMSD of Protein-H+ligand
Which one would you recommend ( 1., 2., and 2.choice)?

Thanks
**

-- 
Ahmet YILDIRIM
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[gmx-users] g_helix and g_rotacf

[simon sham]

Hi,
I have two questions about using g-helix and g_rotacf
On g_helix,
1. I have used the following command:
    "g_helix -s md.tpr -f md.xtc -n index.ndx -b 1 -e 2"
    In the index file, I have residues 10-20 as my group.
    However, when I ran the above command, I did not have the n-ahx.xvg file.
    Did I miss something here?
On g_rotacf,
    I have used the following commands to calculate the order parameters:
    "trjconv -s md.tpr -f noPBC.xtc -o fit.xtc -fit rot+trans" to remove the 
rotational and 
    translational motion of  my protein.
    " g_rotacf -s md.tpr -f fit.xtc -d -n nh - P 2 ". In the index file, it 
lists all the NH pairs 
    except the N atoms from proline. It gave order.xvg and rotacf.xvg.
    In terms of getting the correct order parameters for each NH, are the above 
2   commands correct?
    Finally, in the manual, it mentions about the triplet, i, j, k. What is the 
meaning of the 
    triplet?

Thanks for your insights!

Simon
     

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Re: [gmx-users] oplsaa vs. charmm

[Mark Abraham]

On 28/05/2011 2:05 AM, Peter C. Lai wrote:

On 2011-05-27 10:50:14AM -0500, simon sham wrote:

Hi,
I have recently done two simulations on a protein at high temperature near its 
melting temperature. At the beginning I used CHARMM forcefield, and then OPLSAA 
to double check the results. There are some differences in the structures 
between the forcefield used.  I know different forcefields can give different 
results. All parameters in the simulations were the same except the forcefield. 
Is there anyway I can tell which forcefield gives more reliable results?


Also you never stated what RMSD/RMSFs between the two and if they are
significant to what you care to see (i.e. if you expect, say, alpha
helix to random coil transition, what changes in the unfolding do you see
that make you suspect one forcefield is better than the other?). Also if this
is in a solvated system, the rest of the forcefield has been parameterized
with the implicit assumption that TIPS3P (Charmm-specific) water will be used
so make sure you have switched your water type when using CHARMM.


Not necessarily required. See http://dx.doi.org/10.1021/ct700053u and 
http://dx.doi.org/10.1021/ct900549r


Mark

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[gmx-users] Re: Velocity autocorrelation function of water using g_velacc

[Andrew DeYoung]

Hi,

I just want to say thank you to everyone who took the time to respond to my
post about the VACF of water.  I really, really appreciate it.  

I made a very silly mistake: I equilibrated the system for 5 ns... only to
throw it all away!  It was a very big mistake on my part, and without your
help, to be honest, I may have blindly gone on making that mistake for a
while, although I hope not.  So, many thanks for your help, and thank you
also for being patient with me.  

Initially my diffusion coefficient via the integral of the VACF (by the
Green-Kubo relation) did not yield the same result as the diffusion
coefficient via the mean square displacement... because I was wrongly
integrating the normalized VACF!  So just in case there are any other
novices reading this mailing list, please don't make the same mistakes I
have.  To obtain the diffusion coefficient from the VACF, be sure to
integrate the UNnormalized VACF, using the option -nonormalize in g_velacc.

Thanks again, 

Andrew DeYoung
Carnegie Mellon University

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Re: [gmx-users] oplsaa vs. charmm

[jalemkul]

Quoting simon sham :


Hi,
Once again, I appreciate all the responses.
1. To correct I just had in the previous email. I used GROMOS53ab  
not CHARMM. My apology.
2. At high temperaure, one of the helical turn in a alpha helix (3  
residues) turns into a coil in GROMOS forcefield throughout the 20ns  
simulation. It was only slightly distorted in OPLSAA simulation in  
20ns.
3. The RMSF (backbone) for those 3 residues: 0.3nm in GROMOS vs. 0.1  
nm in OPLSAA.


As I mentioned, the protein is near its melting temperature,  
therefore, I am not surprised to see some helix to coil transition  
or helical distortions. As Justin has suggested, I probably will try  
to make a longer run to see what will happen.




Gromos96 53a6 shows a bias towards extended configurations, thus  
excessively destabilizing helices.  There are recent papers about this  
phenomenon.  Sort of a huge difference between Gromos96 and CHARMM :)


-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] protein-ligand interaction

[jalemkul]

Quoting ahmet y?ld?r?m :


Dear users,

I want to investigate *Ligand effect *on the protein .
To investigation the interaction of protein-ligand:
*RMSD calculations:*
1.
a) RMSD of Backbone
b) RMSD of Backbone+ligand
2.
a) RMSD of Protein
b) RMSD of Protein+ligand
3.
a) RMSD of Protein-H
b) RMSD of Protein-H+ligand
Which one would you recommend ( 1., 2., and 2.choice)?



Unless the effect of your ligand is very large (i.e., the whole  
protein is significantly more or less stable in the presence of the  
ligand), then likely none of these analyses will be particularly  
illustrative as they are not very sensitive to small changes.  You can  
get a per-residue RMSD by using g_rmsf -od to see the effect of the  
ligand on each residue.  Otherwise, the most common quantity measured  
is backbone RMSD.


-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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[gmx-users] Fwd: request

[Mark Abraham]

Please do not send unsolicited private requests for help. The gmx-users 
mailing list is appropriate. I am forwarding there without the file 
attachments.


You should not mix force fields 
http://www.gromacs.org/Documentation/How-tos/Parameterization


Your actual errors suggest you do not have interaction types defined for 
the interactions specified in your molecule .itp file. You need to do 
your own detective work to find out why.


Mark

 Original Message 
Subject:request
Date:   Fri, 27 May 2011 22:15:21 +0430
From:   mona dehghani 
To: mark.abra...@anu.edu.au



Dear Dr.Abraham
I am a PHD student and I use from  AMBER96FF ,CHARMM27ff ports  in 
GROMACS for simulation . DNA sequence is CGCGAATT(5CM)CGCG.I have 
inserted a new residue (DM instead of 5CM) and changed relative 
files(the attached files).


but I have fatal erorrs in grompp:
{erorr1:[file epo0003-DNA-chain-A.itp ,line 2322]:
No default Angletypes}
{erorr2:[file epo0003-DNA-chain-A.itp ,line 3679]:
No default Improper Dih.types}
{erorr3:[file epo0003-DNA-chain-B.itp ,line 2322]:
No default Angletypes}
{erorr4:[file epo0003-DNA-chain-B.itp ,line 3679]:
No default Improper Dih.types}

Please find the attached files .Kindly help me solve this problem.

I would really appreciate that

Mona Dehghani
Phd student
Institute of Biochemistry and Biophysics


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[gmx-users] Domain Motion => How do get the rotational axis from eigenvectors ?

[Chih-Ying Lin]

Hi
I want to get the rotational axis about the protein domain motion.
*From the DynDom website => "DynDom* is a program to determine domains,
hinge axes and hinge bending residues in proteins where two conformations
are available."

Questions:
1. Do the hinge axes represent the rotational axis about the protein domain
motion ?
2. From its User created database, domains and hinge bending residues,
rotation angles and translation are created.
=> The rotation angles must be defined as the angle of rotation between
two domains based on the hinge axes, right ?
=> The vector of the hinge axes is not given by DynDom website, or I did
not find it ???
=> Hinge axes could be obtained from hinge bending axes residues, right
  If so, How 
=> How can I get the vector of the hinge axes with the results from
DynDom ???
=> I found some papers drawing the hinge axes, can Gromacs help me find
and draw the hinge axes 
=> From User created database in the DynDom website, it is showing
"Sequence". What does sequence represent ???
3. Should I install the program of DynDom and then g_dyndom can be
functioned ???
(we need to install DSSP before using do_dssp)
4. From Gromacs manual => "The purpose of this program (g_dyndom) is to
interpolate and extrapolate the rotation as found by DynDom."
   What does it mean "to interpolate and extrapolate the rotation as found
by DynDom" ?


Thank you
Lin






Message: 1
Date: Thu, 26 May 2011 19:54:29 -0700
From: Chih-Ying Lin 
Subject: [gmx-users] Domain Motion => How do get the rotational axis
   fromeigenvectors ?
To: gmx-users@gromacs.org
Message-ID: 
Content-Type: text/plain; charset="iso-8859-1"

Hi
I want to protein's domain motion.
I use   g_covarandg_anaeig  to get the eigenvectors.
How can i get the rotational axis of which protein do its domain motion from
those eigenvectors?

I found the papers and the authors plot its rotational axis of domain
motion.
How did they make it ?


Thank you
Lin
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Message: 2
Date: Fri, 27 May 2011 05:54:07 +0200
From: Tsjerk Wassenaar 
Subject: Re: [gmx-users] Domain Motion => How do get the rotational
   axis from   eigenvectors ?
To: Discussion list for GROMACS users 
Message-ID: 
Content-Type: text/plain; charset=ISO-8859-1

Hi Lin,

You don't get such axes directly from covariance analysis. If you want
to know which rotations are associated with a certain eigenvector, you
have to run a routine like dyndom (http://fizz.cmp.uea.ac.uk/dyndom/)
on the extreme projections of your trajectory onto an eigenvector.

Cheers,

Tsjerk
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[gmx-users] Minimum periodic distance

[Kavyashree M]

Dear users,

I ran a simulation of a protein in water with rlist = rcoloumb = 1.4nm,
rvdw = 1.0nm, with PME and the distance between in the periodic
was set to a minimum of 2.0 i.,e distance between protein and cell
edge was set to 1.0nm, Even then, when I ran g_mindist, there was
a message stating that  -

"shortest periodic distance is 1.39714 (nm) at time 21824 (ps),
between atoms 2062 and 3688"
where 2062 is a protein atom and 21824 is a water molecule.

I wanted to know why this happens in spite of taking care of it
earlier.

what are the consequences, what is the solution?

Thanking you
kavya
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