[gmx-users] Re: gmx-users Digest, Vol 55, Issue 106
Sunjoo Lee
sunnytov at gmail.com
Wed Nov 19 18:39:58 CET 2008
On Wed, Nov 19, 2008 at 10:20 AM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
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> 1. Re: RE: [gmx-users] sedoheptulose (Bernhard Knapp)
> 2. Re: sedoheptulose (Mark Abraham)
> 3. large charge group (Sunjoo Lee)
> 4. RE: large charge group (Berk Hess)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 19 Nov 2008 16:52:22 +0100
> From: Bernhard Knapp <bernhard.knapp at meduniwien.ac.at>
> Subject: Re: RE: [gmx-users] sedoheptulose
> To: gmx-users at gromacs.org
> Message-ID: <49243636.2050709 at meduniwien.ac.at>
> Content-Type: text/plain; charset="us-ascii"
>
> thanks for the hints but unfortunately i still can not get the molecule
> running. i tried with both prodrg server and x2top but with limited success:
>
> in the first case i generate the gro.pdb and .top file via the
> webinterface [1] of prodrg by pasting my coordinate file into the
> textbox. then i run the following commands:
>
> editconf -f sedoheptulose.gro.pdb -o sedoheptulose.cube.pdb -bt cubic -d 2.0
> genbox -cp sedoheptulose.cube.pdb -cs spc216.gro -o
> sedoheptulose.water.pdb -p sedoheptulose.top -nice 0
> grompp -np 1 -f em.mdp -c sedoheptulose.water.pdb -p sedoheptulose.top
> -o sedoheptulose.em.tpr
>
> but in the grompp commands the following error occurs:
>
> -------------------------------------------------------
> Program grompp, VERSION 3.3.1
> Source code file: topio.c, line: 388
>
> Fatal error:
> Invalid order for directive moleculetype, file ""sedoheptulose.top"",
> line 17
> -------------------------------------------------------
>
> but in line 17 only "[ moleculetype ]" is written?
>
>
>
> in the second case I do not really understand the error message:
>
> x2top -f sedoheptulose.pdb -o sedoheptulose.top
>
> leads to:
>
> -------------------------------------------------------
> Program x2top, VERSION 3.3.1
> Source code file: futil.c, line: 537
>
> Fatal error:
> Library file ffG43a1.n2t not found in current dir nor in default
> directories.
> (You can set the directories to search with the GMXLIB path variable)
> -------------------------------------------------------
>
>
> also in the faq i could not find a real guide how to simulate such a
> molecule ...
>
>
>
> Bernhard
>
>
>
>
> [1] http://davapc1.bioch.dundee.ac.uk/prodrg/index.html
>
>
>
> gmx-users-request at gromacs.org wrote:
>
>>Message: 1
>>Date: Wed, 19 Nov 2008 13:25:07 +0000
>>From: "Kukol, Andreas" <a.kukol at herts.ac.uk>
>>Subject: RE: [gmx-users] sedoheptulose
>>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>Message-ID:
>> <2F848DC922C8D741BF3A60B7D7108B6A7C6BD2D23B at UH-MAILSTOR.herts.ac.uk>
>>Content-Type: text/plain; charset="iso-8859-1"
>>
>>Yes, it is possible by deveoping your own topology. Pdb2gmx is not suitable for that purpose.
>>
>>It would be helpful to check out the documentation resources and manual, e.g.
>>
>>http://wiki.gromacs.org/index.php/FAQs
>>
>>x2top and the prodgr web-server might be some good starting points.
>>
>>Andreas
>>
>>
>>
>>From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Bernhard Knapp
>>Sent: 19 November 2008 12:54
>>To: gmx-users at gromacs.org
>>Subject: [gmx-users] sedoheptulose
>>
>>Dear users
>>
>>I would like to perform a MD simulation of Sedoheptulose (C7H14O7) via Gromacs. But already during pdb2gmx it comes up with:
>>"Residue 'UNK' not found in residue topology database" which is obviously clear since sedoheptulose is not an amino acid. Is it somehow possible to simulate this molecule?
>>
>>the sedoheptulose data to start from is:
>>ATOM 1 C UNK 0 -3.442 2.742 0.000 0.00 0.00 C+0
>>ATOM 2 C UNK 0 -2.108 3.512 0.000 0.00 0.00 C+0
>>ATOM 3 C UNK 0 -0.774 2.742 0.000 0.00 0.00 C+0
>>ATOM 4 C UNK 0 0.559 3.512 0.000 0.00 0.00 C+0
>>ATOM 5 C UNK 0 1.893 2.742 0.000 0.00 0.00 C+0
>>ATOM 6 C UNK 0 3.227 3.512 0.000 0.00 0.00 C+0
>>ATOM 7 O UNK 0 -0.774 1.202 0.000 0.00 0.00 O+0
>>ATOM 8 O UNK 0 0.559 5.052 0.000 0.00 0.00 O+0
>>ATOM 9 O UNK 0 1.893 1.202 0.000 0.00 0.00 O+0
>>ATOM 10 O UNK 0 -4.775 3.512 0.000 0.00 0.00 O+0
>>ATOM 11 O UNK 0 -2.108 5.052 0.000 0.00 0.00 O+0
>>ATOM 12 H UNK 0 -6.109 2.742 0.000 0.00 0.00 H+0
>>ATOM 13 H UNK 0 -0.774 5.822 0.000 0.00 0.00 H+0
>>ATOM 14 H UNK 0 1.893 5.822 0.000 0.00 0.00 H+0
>>ATOM 15 H UNK 0 0.559 0.432 0.000 0.00 0.00 H+0
>>ATOM 16 H UNK 0 3.227 0.432 0.000 0.00 0.00 H+0
>>ATOM 17 C UNK 0 4.560 2.742 0.000 0.00 0.00 C+0
>>ATOM 18 O UNK 0 5.894 3.512 0.000 0.00 0.00 O+0
>>ATOM 19 H UNK 0 7.228 2.742 0.000 0.00 0.00 H+0
>>ATOM 20 O UNK 0 3.227 5.052 0.000 0.00 0.00 O+0
>>
>>cheers
>>bernhard
>>
>>
>>
>>
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> ------------------------------
>
> Message: 2
> Date: Thu, 20 Nov 2008 03:04:29 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] sedoheptulose
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4924390D.4040303 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Bernhard Knapp wrote:
>> thanks for the hints but unfortunately i still can not get the molecule
>> running. i tried with both prodrg server and x2top but with limited success:
>>
>> in the first case i generate the gro.pdb and .top file via the
>> webinterface [1] of prodrg by pasting my coordinate file into the
>> textbox. then i run the following commands:
>>
>> editconf -f sedoheptulose.gro.pdb -o sedoheptulose.cube.pdb -bt cubic -d 2.0
>> genbox -cp sedoheptulose.cube.pdb -cs spc216.gro -o
>> sedoheptulose.water.pdb -p sedoheptulose.top -nice 0
>> grompp -np 1 -f em.mdp -c sedoheptulose.water.pdb -p sedoheptulose.top
>> -o sedoheptulose.em.tpr
>>
>> but in the grompp commands the following error occurs:
>>
>> -------------------------------------------------------
>> Program grompp, VERSION 3.3.1
>> Source code file: topio.c, line: 388
>>
>> Fatal error:
>> Invalid order for directive moleculetype, file ""sedoheptulose.top"",
>> line 17
>> -------------------------------------------------------
>>
>> but in line 17 only "[ moleculetype ]" is written?
>
> This error really means what it says - this directive is given at a time
> when it is not valid. You'll need to understand the .top file format,
> which is explained with an example in section 5.7 of the manual. It
> sounds like you should try out some tutorial material to get a handle on
> some of the GROMACS ways of doing things.
>
>> also in the faq i could not find a real guide how to simulate such a
>> molecule ...
>
> Developing a topology for a "new" molecule is not a good starting place
> for a near-beginner with any MD package. You will need to read relevant
> parts of the manual thoroughly.
>
> Mark
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 19 Nov 2008 10:01:01 -0600
> From: "Sunjoo Lee" <sunnytov at gmail.com>
> Subject: [gmx-users] large charge group
> To: gmx-users at gromacs.org
> Message-ID:
> <39fb0dd50811190801s789101cau9b506769ff495ca0 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hello All
>
> Recently I have figured out the biggest problem that made my system unstable.
> I have parameterized a molecule pretty similar to octane. A single
> charge group used to be assigned to this molecule. With 1 nm cut-off
> distance for LJ interaction and the direct space for electrostatic
> interaction, the system underwent severe volume fluctuation and at the
> end crashed due to enormously large short range coulomb interaction
> energy. The problem was temporarily resolved by using greater cut-off
> distance such as 1.4 nm. But this fixation was not perfect when I put
> this molecule into more complex system. Regardless of the cut-off
> distance even to 1.8 nm did not solve the problem. The simulation
> always terminated due to large coulomb energy even though no direct
> contact or any weird structure was observed at that snapshot.
>
> With the help of many experts, I have made a single charge group into
> three smaller charge group, which magically fixed all the problem that
> I have had for almost 2 years. I know that charge group is only used
> for neighbor search. Can anybody tell me how the size of charge group
> can influence the interaction between atoms depending on the
> complexity of the system and cut-off distance??
>
> Thank you in advance
>
> Sunjoo
>
>
> ------------------------------
Hello Berk
Thank you for the clear explanation.
It makes very good sense what was the problem!
Thank you
Sunjoo
>
> Message: 4
> Date: Wed, 19 Nov 2008 17:15:24 +0100
> From: Berk Hess <gmx3 at hotmail.com>
> Subject: RE: [gmx-users] large charge group
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <BLU134-W454C6DBBB1B9D867D3B1BA8E0D0 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Hi,
>
> The charge groups "only" affect the neighbor searching,
> which in practice means they affect everything.
>
> In Gromacs atoms in two different charge groups will only interactions
> when the center of geometry of the two charge groups is within rlist.
>
> The worst case scenario, which has happend to several people, is:
> A molecule with a radius of about 0.5 nm is one charge group.
> If the cut-off is 1 nm, two molecules will only really start interacting
> when they already overlap.
>
> In 4.0 I put a check on large charge groups.
> If you have charge groups of more than 10 atoms, grompp will now
> warn you with:
> "The largest charge group contains %d atoms.\n"
> "Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts.\n"
> "For efficiency and accuracy, charge group should consist of a few atoms.\n"
> "For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.\n",
>
> Berk
>
>> Date: Wed, 19 Nov 2008 10:01:01 -0600
>> From: sunnytov at gmail.com
>> To: gmx-users at gromacs.org
>> Subject: [gmx-users] large charge group
>>
>> Hello All
>>
>> Recently I have figured out the biggest problem that made my system unstable.
>> I have parameterized a molecule pretty similar to octane. A single
>> charge group used to be assigned to this molecule. With 1 nm cut-off
>> distance for LJ interaction and the direct space for electrostatic
>> interaction, the system underwent severe volume fluctuation and at the
>> end crashed due to enormously large short range coulomb interaction
>> energy. The problem was temporarily resolved by using greater cut-off
>> distance such as 1.4 nm. But this fixation was not perfect when I put
>> this molecule into more complex system. Regardless of the cut-off
>> distance even to 1.8 nm did not solve the problem. The simulation
>> always terminated due to large coulomb energy even though no direct
>> contact or any weird structure was observed at that snapshot.
>>
>> With the help of many experts, I have made a single charge group into
>> three smaller charge group, which magically fixed all the problem that
>> I have had for almost 2 years. I know that charge group is only used
>> for neighbor search. Can anybody tell me how the size of charge group
>> can influence the interaction between atoms depending on the
>> complexity of the system and cut-off distance??
>>
>> Thank you in advance
>>
>> Sunjoo
>> _______________________________________________
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