hi,<br>According to the help frm gmx-users ,<br>I did editconf with -center option twice.concatenated the coordinate files using cat.<br>Then i ran frm pdb2gmx till genbox..When I saw result pdb using pymol there was only one protein inside the box.Why is it like that?When i opened the gro file after pdb2gmx number of atoms were double than the original one.<br>
wht would be the problem?please help<br>These are the commands which i performed:<br><br>pdb2gmx -f 1lyd.pdb -o lyzo<br>editconf -f lyzo -bt cubic -d 1 -center 1 -o lyzo_edit.pdb<br>editconf -f lyzo -bt cubic -d 1 -center 1 -o lyzo_edit1.pdb<br>
cat lyzo_edit.pdb lyzo_edit1.pdb > lyzozym.pdb<br>pdb2gmx -f lyzozym.pdb -o lyzozy<br>editconf -f lyzozy -bt cubic -d 1 -center 1 -o lyzozy_edit -c<br>genbox -cp lyzozy_edit -cs spc216 -o lyzozy_gen.pdb<br><br>Thanks in advance<br>
<br>smriti<br><br><div class="gmail_quote">On Tue, Jul 26, 2011 at 8:09 PM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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Today's Topics:<br>
<br>
1. Re: multiple protein interaction (Justin A. Lemkul)<br>
2. Re: OPLS for group -N=CH2 (Justin A. Lemkul)<br>
3. genconf and bonded interactions (Fabio Affinito)<br>
4. Re: genconf and bonded interactions (Justin A. Lemkul)<br>
5. Re: genconf and bonded interactions (Fabio Affinito)<br>
6. Re: genconf and bonded interactions (Justin A. Lemkul)<br>
7. Re: genconf and bonded interactions (Fabio Affinito)<br>
8. Re: genconf and bonded interactions (Justin A. Lemkul)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 26 Jul 2011 07:39:05 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] multiple protein interaction<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4E2EA759.30207@vt.edu">4E2EA759.30207@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
smriti Sebastian wrote:<br>
> hi all,<br>
> I am new to GROMACS.I would like to know how we will simulate putting<br>
> more than two or more molecules of same proteins inside the box and do<br>
> simulation?Is there any possibility to replace 100 atoms or so of<br>
> solvent with proteins?<br>
> Please help.<br>
><br>
<br>
You received two replies the last time you asked this exact same question:<br>
<br>
<a href="http://lists.gromacs.org/pipermail/gmx-users/2011-July/063145.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2011-July/063145.html</a><br>
<a href="http://lists.gromacs.org/pipermail/gmx-users/2011-July/063146.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2011-July/063146.html</a><br>
<br>
So what have you done to try to proceed? If you want free help, you have to be<br>
willing to use what you're given to make some progress and report back with<br>
specific issues that arise.<br>
<br>
-Justin<br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Tue, 26 Jul 2011 07:41:22 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] OPLS for group -N=CH2<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4E2EA7E2.7090907@vt.edu">4E2EA7E2.7090907@vt.edu</a>><br>
Content-Type: text/plain; charset=UTF-8; format=flowed<br>
<br>
<br>
<br>
<a href="mailto:bhf70@udsu.ru">bhf70@udsu.ru</a> wrote:<br>
> Dear users.<br>
><br>
> Help me.<br>
> What parametres of force field OPLS it is necessary to be used<br>
> for group -N=CH2 (imine group) ?<br>
><br>
<br>
Check out the OPLS papers for suitable groups or atom types that are present,<br>
and if there's nothing already there, then you'll have to parameterize the group<br>
yourself (not a novice exercise):<br>
<br>
<a href="http://www.gromacs.org/Documentation/How-tos/Parameterization" target="_blank">http://www.gromacs.org/Documentation/How-tos/Parameterization</a><br>
<br>
-Justin<br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Tue, 26 Jul 2011 15:59:14 +0200 (CEST)<br>
From: Fabio Affinito <<a href="mailto:f.affinito@cineca.it">f.affinito@cineca.it</a>><br>
Subject: [gmx-users] genconf and bonded interactions<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4E2EC831.7000209@cineca.it">4E2EC831.7000209@cineca.it</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
Hi all,<br>
I used genconf because I wanted to replicate a membrane with ion channel<br>
on the xy plane:<br>
genconf -f conf.gro -o out.gro -nbox 2 2 1<br>
<br>
Then I edited by hand the .top file where I modified the number of<br>
molecules in the system.<br>
<br>
When attempting to run, disregarding the number of processors, the mdrun<br>
crashes because domain decomposition fails.<br>
Looking with attention to the log I find this:<br>
> Initializing Domain Decomposition on 4096 nodes<br>
> Dynamic load balancing: auto<br>
> Will sort the charge groups at every domain (re)decomposition<br>
> Initial maximum inter charge-group distances:<br>
> two-body bonded interactions: 30.871 nm, LJ-14, atoms 193657 193660<br>
> multi-body bonded interactions: 30.871 nm, Angle, atoms 193656 193659<br>
> Minimum cell size due to bonded interactions: 33.959 nm<br>
> Maximum distance for 7 constraints, at 120 deg. angles, all-trans: 1.139 nm<br>
> Estimated maximum distance required for P-LINCS: 1.139 nm<br>
> Guess for relative PME load: 0.44<br>
> Will use 2304 particle-particle and 1792 PME only nodes<br>
> This is a guess, check the performance at the end of the log file<br>
> Using 1792 separate PME nodes<br>
> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25<br>
> Optimizing the DD grid for 2304 cells with a minimum initial size of 42.448 nm<br>
> The maximum allowed number of cells is: X 1 Y 1 Z 0<br>
<br>
Now, I'm wondering why do I have such big bond interation length.. 31nm!<br>
I guess that the problems in the DD arises from this.<br>
<br>
Can you give me some suggestions?<br>
<br>
Thanks in advance,<br>
<br>
Fabio<br>
<br>
--<br>
Fabio Affinito, PhD<br>
SuperComputing Applications and Innovation Department<br>
CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY<br>
Tel: +39 051 6171794 Fax: +39 051 6132198<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Tue, 26 Jul 2011 10:19:28 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] genconf and bonded interactions<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4E2ECCF0.6080506@vt.edu">4E2ECCF0.6080506@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Fabio Affinito wrote:<br>
> Hi all,<br>
> I used genconf because I wanted to replicate a membrane with ion channel<br>
> on the xy plane:<br>
> genconf -f conf.gro -o out.gro -nbox 2 2 1<br>
><br>
> Then I edited by hand the .top file where I modified the number of<br>
> molecules in the system.<br>
><br>
> When attempting to run, disregarding the number of processors, the mdrun<br>
> crashes because domain decomposition fails.<br>
> Looking with attention to the log I find this:<br>
>> Initializing Domain Decomposition on 4096 nodes<br>
>> Dynamic load balancing: auto<br>
>> Will sort the charge groups at every domain (re)decomposition<br>
>> Initial maximum inter charge-group distances:<br>
>> two-body bonded interactions: 30.871 nm, LJ-14, atoms 193657 193660<br>
>> multi-body bonded interactions: 30.871 nm, Angle, atoms 193656 193659<br>
>> Minimum cell size due to bonded interactions: 33.959 nm<br>
>> Maximum distance for 7 constraints, at 120 deg. angles, all-trans:<br>
>> 1.139 nm<br>
>> Estimated maximum distance required for P-LINCS: 1.139 nm<br>
>> Guess for relative PME load: 0.44<br>
>> Will use 2304 particle-particle and 1792 PME only nodes<br>
>> This is a guess, check the performance at the end of the log file<br>
>> Using 1792 separate PME nodes<br>
>> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25<br>
>> Optimizing the DD grid for 2304 cells with a minimum initial size<br>
>> of 42.448 nm<br>
>> The maximum allowed number of cells is: X 1 Y 1 Z 0<br>
><br>
> Now, I'm wondering why do I have such big bond interation length.. 31nm!<br>
> I guess that the problems in the DD arises from this.<br>
><br>
> Can you give me some suggestions?<br>
><br>
<br>
Were the molecules whole in the coordinate file you replicated? If not, the<br>
bonds will now be assigned across the entire box.<br>
<br>
-Justin<br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Tue, 26 Jul 2011 16:28:17 +0200 (CEST)<br>
From: Fabio Affinito <<a href="mailto:f.affinito@cineca.it">f.affinito@cineca.it</a>><br>
Subject: Re: [gmx-users] genconf and bonded interactions<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <<a href="mailto:4E2ECF00.8080206@cineca.it">4E2ECF00.8080206@cineca.it</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
On 07/26/2011 04:19 PM, Justin A. Lemkul wrote:<br>
<br>
><br>
> Were the molecules whole in the coordinate file you replicated? If not,<br>
> the bonds will now be assigned across the entire box.<br>
><br>
> -Justin<br>
><br>
Yes and not, depending on what you mean by "whole".<br>
It is an ion channel, so it's made of four chains.<br>
This clarifies? (i guess not..)<br>
<br>
F<br>
<br>
--<br>
Fabio Affinito, PhD<br>
SuperComputing Applications and Innovation Department<br>
CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY<br>
Tel: +39 051 6171794 Fax: +39 051 6132198<br>
<br>
<br>
------------------------------<br>
<br>
Message: 6<br>
Date: Tue, 26 Jul 2011 10:30:07 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] genconf and bonded interactions<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4E2ECF6F.20707@vt.edu">4E2ECF6F.20707@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Fabio Affinito wrote:<br>
> On 07/26/2011 04:19 PM, Justin A. Lemkul wrote:<br>
><br>
>><br>
>> Were the molecules whole in the coordinate file you replicated? If not,<br>
>> the bonds will now be assigned across the entire box.<br>
>><br>
>> -Justin<br>
>><br>
> Yes and not, depending on what you mean by "whole".<br>
> It is an ion channel, so it's made of four chains.<br>
> This clarifies? (i guess not..)<br>
<br>
By whole, I mean that the molecules are not split across periodic boundaries in<br>
the initial configuration that you replicated. If you replicate a periodic<br>
break, then you split the molecules by a distance equal to the new periodic<br>
distance.<br>
<br>
-Justin<br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 7<br>
Date: Tue, 26 Jul 2011 16:35:58 +0200 (CEST)<br>
From: Fabio Affinito <<a href="mailto:f.affinito@cineca.it">f.affinito@cineca.it</a>><br>
Subject: Re: [gmx-users] genconf and bonded interactions<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <<a href="mailto:4E2ED0CE.9060009@cineca.it">4E2ED0CE.9060009@cineca.it</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
On 07/26/2011 04:30 PM, Justin A. Lemkul wrote:<br>
><br>
><br>
> Fabio Affinito wrote:<br>
>> On 07/26/2011 04:19 PM, Justin A. Lemkul wrote:<br>
>><br>
>>><br>
>>> Were the molecules whole in the coordinate file you replicated? If not,<br>
>>> the bonds will now be assigned across the entire box.<br>
>>><br>
>>> -Justin<br>
>>><br>
>> Yes and not, depending on what you mean by "whole".<br>
>> It is an ion channel, so it's made of four chains.<br>
>> This clarifies? (i guess not..)<br>
><br>
> By whole, I mean that the molecules are not split across periodic<br>
> boundaries in the initial configuration that you replicated. If you<br>
> replicate a periodic break, then you split the molecules by a distance<br>
> equal to the new periodic distance.<br>
><br>
> -Justin<br>
><br>
Ok, so: no, it's not broken.<br>
<br>
<br>
--<br>
Fabio Affinito, PhD<br>
SuperComputing Applications and Innovation Department<br>
CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY<br>
Tel: +39 051 6171794 Fax: +39 051 6132198<br>
<br>
<br>
------------------------------<br>
<br>
Message: 8<br>
Date: Tue, 26 Jul 2011 10:38:12 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] genconf and bonded interactions<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4E2ED154.3040502@vt.edu">4E2ED154.3040502@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Fabio Affinito wrote:<br>
> On 07/26/2011 04:30 PM, Justin A. Lemkul wrote:<br>
>><br>
>><br>
>> Fabio Affinito wrote:<br>
>>> On 07/26/2011 04:19 PM, Justin A. Lemkul wrote:<br>
>>><br>
>>>><br>
>>>> Were the molecules whole in the coordinate file you replicated? If not,<br>
>>>> the bonds will now be assigned across the entire box.<br>
>>>><br>
>>>> -Justin<br>
>>>><br>
>>> Yes and not, depending on what you mean by "whole".<br>
>>> It is an ion channel, so it's made of four chains.<br>
>>> This clarifies? (i guess not..)<br>
>><br>
>> By whole, I mean that the molecules are not split across periodic<br>
>> boundaries in the initial configuration that you replicated. If you<br>
>> replicate a periodic break, then you split the molecules by a distance<br>
>> equal to the new periodic distance.<br>
>><br>
>> -Justin<br>
>><br>
> Ok, so: no, it's not broken.<br>
><br>
<br>
What you need to do is use the information mdrun provided you to diagnose what's<br>
going on. Apparently atoms 193657 193660 are separated by 31 nm. What are your<br>
box vectors? Where are these atoms in the system? Then you'll have your<br>
answer. The only reason I can think of for such extreme distances is a<br>
periodicity issue.<br>
<br>
-Justin<br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
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End of gmx-users Digest, Vol 87, Issue 138<br>
******************************************<br>
</font></blockquote></div><br>