date:20160724

Re: [gmx-users] Error in energy groups

2016-07-24 Thread masoud keramati

it was wrong
i make new index that contain Non-Protein group.
my problem fix!

tnx

On Mon, Jul 25, 2016 at 12:08 AM, masoud keramati  wrote:

> tnx Dr.Lemkul
>
> yes the problem was in the tc-grps.
> tc-grps= Protein Non-Protein
> and there is no Non-Protein group in index file.
> it's true that i use System for tc-grps?
>
> On Sun, Jul 24, 2016 at 11:54 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 7/24/16 3:17 PM, masoud keramati wrote:
>>
>>> Hi all
>>>
>>> i have a protein with six chain.
>>> i create an index file that include each chain (chA chB ..)
>>> in mdp file i define energy groups such that:
>>> energygrps   = chA chD
>>>
>>> for grompp i used this command:
>>> gmx grompp -f md.mdp -c npt.gro -n chains.ndx -p topol.top -o A-D.tpr
>>>
>>> but i got this error:
>>> "Group Non-Protein referenced in the .mdp file was not found in the index
>>> file.
>>> Group names must match either [moleculetype] names or custom index group
>>> names, in which case you must supply an index file to the '-n' option
>>> of grompp "
>>>
>>> what's wrong with this?!
>>>
>>>
>> You have some setting that uses Non-Protein but you haven't got that in
>> your index file.  Check tc-grps as the most likely culprit.  If your index
>> file *only* contains the chains that you've specified, then you're going to
>> encounter problems.  In general, add groups that you need and leave the
>> default groups (System, Protein, Non-Protein, etc.) in place for ease of
>> use.
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
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>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
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Re: [gmx-users] Error in energy groups

2016-07-24 Thread masoud keramati

tnx Dr.Lemkul

yes the problem was in the tc-grps.
tc-grps= Protein Non-Protein
and there is no Non-Protein group in index file.
it's true that i use System for tc-grps?

On Sun, Jul 24, 2016 at 11:54 PM, Justin Lemkul  wrote:

>
>
> On 7/24/16 3:17 PM, masoud keramati wrote:
>
>> Hi all
>>
>> i have a protein with six chain.
>> i create an index file that include each chain (chA chB ..)
>> in mdp file i define energy groups such that:
>> energygrps   = chA chD
>>
>> for grompp i used this command:
>> gmx grompp -f md.mdp -c npt.gro -n chains.ndx -p topol.top -o A-D.tpr
>>
>> but i got this error:
>> "Group Non-Protein referenced in the .mdp file was not found in the index
>> file.
>> Group names must match either [moleculetype] names or custom index group
>> names, in which case you must supply an index file to the '-n' option
>> of grompp "
>>
>> what's wrong with this?!
>>
>>
> You have some setting that uses Non-Protein but you haven't got that in
> your index file.  Check tc-grps as the most likely culprit.  If your index
> file *only* contains the chains that you've specified, then you're going to
> encounter problems.  In general, add groups that you need and leave the
> default groups (System, Protein, Non-Protein, etc.) in place for ease of
> use.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Error in energy groups

2016-07-24 Thread Justin Lemkul




On 7/24/16 3:17 PM, masoud keramati wrote:

Hi all

i have a protein with six chain.
i create an index file that include each chain (chA chB ..)
in mdp file i define energy groups such that:
energygrps   = chA chD

for grompp i used this command:
gmx grompp -f md.mdp -c npt.gro -n chains.ndx -p topol.top -o A-D.tpr

but i got this error:
"Group Non-Protein referenced in the .mdp file was not found in the index
file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp "

what's wrong with this?!



You have some setting that uses Non-Protein but you haven't got that in your 
index file.  Check tc-grps as the most likely culprit.  If your index file 
*only* contains the chains that you've specified, then you're going to encounter 
problems.  In general, add groups that you need and leave the default groups 
(System, Protein, Non-Protein, etc.) in place for ease of use.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Error in energy groups

2016-07-24 Thread masoud keramati

Hi all

i have a protein with six chain.
i create an index file that include each chain (chA chB ..)
in mdp file i define energy groups such that:
energygrps   = chA chD

for grompp i used this command:
gmx grompp -f md.mdp -c npt.gro -n chains.ndx -p topol.top -o A-D.tpr

but i got this error:
"Group Non-Protein referenced in the .mdp file was not found in the index
file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp "

what's wrong with this?!

thank for your help : )
-- 
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Re: [gmx-users] Analyzing trajectory file always stops.

2016-07-24 Thread Mark Abraham

Hi,

That usually means you are working in a filesystem like FAT32 that cannot
access files greater than 2GB. If so, try a real one :-)

Mark

On Sun, 24 Jul 2016 12:53 yamashita.ryoto@st.kyoto-u.ac.jp <
yamashita.ryoto@st.kyoto-u.ac.jp> wrote:

>
> Dear Mr.Lemkul
> >How large is your trajectory?  How much memory do you have >available?
> Does
> >reducing the frame interval with trjconv work?
>
> Thank you for commenting.
> My trajectory file is 109GB.(1000 steps)
> According to the command vmstat, avm is 1044MB( and fre is 616MB).
> reducing the frame interval with trjconv also stops
> It stops at the same Reading frame 1100.
> (I'm sorry,  I correct the wrong information that analyzing stops at not
> two thirds but one 1th of my file.)
> the command is
> gmx_mpi_d trjconv -f oligomer.tpr.trr -s oligomer.tpr -dt 1 -o test.trr
>
> Thanks,
> Yamashita
>
> 
> 差出人: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> が Justin Lemkul <
> jalem...@vt.edu> の代理で送信
> 送信日時: 2016年7月22日 20:34:31
> 宛先: gmx-us...@gromacs.org
> 件名: Re: [gmx-users] Analyzing trajectory file always stops.
>
>
>
> On 7/21/16 9:19 PM, yamashita.ryoto@st.kyoto-u.ac.jp wrote:
> > Dear all.
> > I have a trouble when analyzing my trajectory file.
> > I want to calculate the radius of gyration of oligomer.But when
> calculating the radius of gyration, the calculations always stop at about
> two thirds of my trajectory file.
> > Could you tell me what is happening if you know?
> >
>
> How large is your trajectory?  How much memory do you have available?  Does
> reducing the frame interval with trjconv work?
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> Justin A. Lemkul - MacKerell Lab
> mackerell.umaryland.edu
> Welcome to my site! To learn more about me and the work I am doing, please
> use the navigation links above.
>
>
>
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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>
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Re: [gmx-users] Analyzing trajectory file always stops.

2016-07-24 Thread yamashita.ryoto....@st.kyoto-u.ac.jp

Dear Mr.Lemkul
>How large is your trajectory?  How much memory do you have >available?  Does
>reducing the frame interval with trjconv work?

Thank you for commenting.
My trajectory file is 109GB.(1000 steps)
According to the command vmstat, avm is 1044MB( and fre is 616MB).
reducing the frame interval with trjconv also stops
It stops at the same Reading frame 1100.
(I'm sorry,  I correct the wrong information that analyzing stops at not two 
thirds but one 1th of my file.)
the command is
gmx_mpi_d trjconv -f oligomer.tpr.trr -s oligomer.tpr -dt 1 -o test.trr

Thanks,
Yamashita

差出人: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 が Justin Lemkul 
 の代理で送信
送信日時: 2016年7月22日 20:34:31
宛先: gmx-us...@gromacs.org
件名: Re: [gmx-users] Analyzing trajectory file always stops.

On 7/21/16 9:19 PM, yamashita.ryoto@st.kyoto-u.ac.jp wrote:
> Dear all.
> I have a trouble when analyzing my trajectory file.
> I want to calculate the radius of gyration of oligomer.But when calculating 
> the radius of gyration, the calculations always stop at about two thirds of 
> my trajectory file.
> Could you tell me what is happening if you know?
>

How large is your trajectory?  How much memory do you have available?  Does
reducing the frame interval with trjconv work?

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
Justin A. Lemkul - MacKerell Lab
mackerell.umaryland.edu
Welcome to my site! To learn more about me and the work I am doing, please use 
the navigation links above.

==
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Re: [gmx-users] Error in energy groups

Re: [gmx-users] Error in energy groups

Re: [gmx-users] Error in energy groups

[gmx-users] Error in energy groups

Re: [gmx-users] Analyzing trajectory file always stops.

Re: [gmx-users] Analyzing trajectory file always stops.

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