[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ï¼
您在 2010å¹´10月9日，18:54:33 写é“:
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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 å“å’¿?<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!
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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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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