[gmx-users] Re: gmx-users Digest, Vol 78, Issue 52

tjmu_hacker at yahoo.com.cn tjmu_hacker at yahoo.com.cn
Sat Oct 9 17:05:15 CEST 2010


Gmx-users-request,您好!

您在 2010年10月9日,18:54:33 写道:

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> Today's Topics:

>    1. output force (???? ?????)
>    2. Re: output force (Mark Abraham)
>    3. Re: how to write a rtp file for amido amine (Mark Abraham)


> ----------------------------------------------------------------------

> Message: 1
> Date: Sat, 9 Oct 2010 14:40:02 +0400
> From: ???? ????? <magistrpetrus at gmail.com>
> Subject: [gmx-users] output force
> To: gmx-users at gromacs.org
> Message-ID:
>         <AANLkTinUm8y=M9dBpjKVH5pmr_zuK_k3uEc81cYUbSXj at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"

> Hello dear gmx-users!

> When calculated forces in gromacs to produce pmf, we have the net force in
> output. For example:
> ...
> #
> # Giving Russians Opium May Alter Current Situation
> #
> @    title "Pull force"
> @    xaxis  label "Time (ps)"
> @    yaxis  label "Force (kJ/mol/nm)"
> @TYPE xy
> 0.000000                1017490.761270
> 0.002000                -253098.034916
> 0.004000                -43856.400160
> 0.006000                48980.619113
> 0.008000                52103.053067
> 0.010000                33788.090031
> 0.012000                19096.388350
> 0.014000                14094.738810
> 0.016000                14027.621966
> 0.018000                15162.993741
> 0.020000                14136.978177
> ... etc.

> What sould I do to get the net force of protein-solvent interactions or
> protein-protein interactions or solvent-solvent interactions instead and get
> output .xvg file in the form like this:

> time     Force(type1)    Force(type2)    Force(type3)

> t1         f1                   f1                    f1
> t2         f2                   f2                    f2
> t3         f3                   f3                    f3
> ...        ...                   ...                    ...
> etc.

> Thank you for attention and I hope you will help me!
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> ------------------------------

> Message: 2
> Date: Sat, 09 Oct 2010 21:50:10 +1100
> From: Mark Abraham <mark.abraham at anu.edu.au>
> Subject: Re: [gmx-users] output force
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <fbe6fea12e6a6.4cb0e392 at anu.edu.au>
> Content-Type: text/plain; charset="iso-8859-5"

> You can get that with cunning use of energy groups and mdrun -rerun, but not mid-simulation.
> Mark  

> ----- Original Message -----
> From: 空忄 哭咿?<magistrpetrus at gmail.com>
> Date: Saturday, October 9, 2010 21:41
> Subject: [gmx-users] output force
> To: gmx-users at gromacs.org

>> Hello dear gmx-users!
>> 
>> When calculated forces in gromacs to produce pmf, we have the net force in output. For example:
>> ...
>> #
>> # Giving Russians Opium May Alter Current Situation
>> #
>> @    title "Pull force"
>>  @    xaxis  label "Time (ps)"
>> @    yaxis  label "Force (kJ/mol/nm)"
>> @TYPE xy
>> 0.000000                1017490.761270
>> 0.002000                -253098.034916
>> 0.004000                -43856.400160
>>  0.006000                48980.619113
>> 0.008000                52103.053067
>> 0.010000                33788.090031
>> 0.012000                19096.388350
>> 0.014000                14094.738810
>> 0.016000                14027.621966
>>  0.018000                15162.993741
>> 0.020000                14136.978177
>> ... etc.
>> 
>> What sould I do to get the net force of protein-solvent interactions or protein-protein interactions or solvent-solvent interactions instead and get output .xvg file in the form like this:
 >> 
>> time     Force(type1)    Force(type2)    Force(type3)
>> 
>> t1         f1                   f1                    f1
>> t2         f2                   f2                    f2
>> t3         f3                   f3                    f3
>>  ...        ...                   ...                    ...
>> etc.
>> 
>> Thank you for attention and I hope you will help me!
 >> -- 
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> ------------------------------

> Message: 3
> Date: Sat, 09 Oct 2010 21:53:41 +1100
> From: Mark Abraham <mark.abraham at anu.edu.au>
> Subject: Re: [gmx-users] how to write a rtp file for amido amine
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <fbdb87472f446.4cb0e465 at anu.edu.au>
> Content-Type: text/plain; charset="us-ascii"



> ----- Original Message -----
> From: lammps lammps <lammp2forum at gmail.com>
> Date: Saturday, October 9, 2010 19:27
> Subject: [gmx-users] how to write a rtp file for amido amine
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>

>> Hi everybody,
>> 
>> I want to use pdb2gmx command to create a .gro file and a .top file for PAMAM whose repeat unit is amidoamine ( attached ).
>> 
>>                                                 /
>> ---CH2--CH2--CO-NH-CH2-CH2-N    (see the attached figure)
>>                                                  \
>> 
>> The atom N have two same branches with --CH2--. I write the rtp file for it as follows:
>> 
>>  [ atoms ]
>>    C1    opls_245    -0.050    1   
>>  .........
>>  [ bonds ]
>>     C1    -N7
>> .......
>>    C6    N7
>>    N7    +C1>    N7    +C1
>> 
>> It seems not work, which gives a wrong top structure. The question is how can I deal with the two branches of N. Any suggestion is appreciated. 

> pdb2gmx is intended only for work with linear heteropolymers. Any
> more complex things (e.g. disulfides, branched structures) have to
> be engineered using the specbonds.dat mechanism.

> Mark

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