[gmx-users] gromacs.org_gmx-users Digest, Vol 190, Issue 31
Shi Hailong
shihailong2019 at gmail.com
Sat Feb 15 21:21:48 CET 2020
> On Feb 15, 2020, at 10:44 AM, gromacs.org_gmx-users-request at maillist.sys.kth.se wrote:
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> Today's Topics:
>
> 1. Re: problem while calculating order parameter (Justin Lemkul)
> 2. Re: Trajectory optimization - 2 chains are separated
> (Marwa Abd El Kader)
> 3. Re: problem while calculating order parameter
> (Devargya Chakraborty)
> 4. Re: Trajectory optimization - 2 chains are separated
> (Justin Lemkul)
> 5. Script for looping n simulations (Neena Susan Eappen)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 15 Feb 2020 09:29:48 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] problem while calculating order parameter
> Message-ID: <23e15586-3133-08fc-0086-2f0a455ddc71 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 2/15/20 4:50 AM, Devargya Chakraborty wrote:
>> i want to calculate the order prameter between two carbon atom namrd C01
>> and C03 in my topology file but while calculating, i am getting the
>> following error.
>
> gmx order is designed to compute deuterium order parameters in alkyl
> chains. It requires special index groups that only contain the atoms of
> interest and those flanking them to define the local molecular axis. See
> http://www.mdtutorials.com/gmx/membrane_protein/09_analysis.html for an
> example.
>
> -Justin
>
>> Taking z axis as normal to the membrane
>> Reading file nvt.tpr, VERSION 2019.1 (single precision)
>> Using following groups:
>> Groupname: System First atomname: C01 First atomnr 0
>> Groupname: Other First atomname: C01 First atomnr 0
>> Groupname: EMI First atomname: C01 First atomnr 0
>> Groupname: NSC First atomname: NBT First atomnr 760
>> Groupname: Water First atomname: OW First atomnr 1360
>> Groupname: SOL First atomname: OW First atomnr 1360
>> Groupname: non-Water First atomname: C01 First atomnr 0
>> Groupname: C01 First atomname: C01 First atomnr 0
>> Groupname: C04 First atomname: C04 First atomnr 1
>> Groupname: C03 First atomname: C03 First atomnr 2
>> Groupname: H07 First atomname: H07 First atomnr 3
>> Groupname: H09 First atomname: H09 First atomnr 4
>> Groupname: H08 First atomname: H08 First atomnr 5
>> Groupname: C05 First atomname: C05 First atomnr 6
>> Groupname: H0B First atomname: H0B First atomnr 7
>> Groupname: H0C First atomname: H0C First atomnr 8
>> Groupname: H0D First atomname: H0D First atomnr 9
>> Groupname: N00 First atomname: N00 First atomnr 10
>> Groupname: C06 First atomname: C06 First atomnr 11
>> Groupname: H0F First atomname: H0F First atomnr 12
>> Groupname: C0N First atomname: C0N First atomnr 13
>> Groupname: H0O First atomname: H0O First atomnr 14
>> Groupname: H0P First atomname: H0P First atomnr 15
>> Groupname: H0Q First atomname: H0Q First atomnr 16
>> Groupname: N02 First atomname: N02 First atomnr 17
>> Groupname: H0E First atomname: H0E First atomnr 18
>> Groupname: NBT First atomname: NBT First atomnr 760
>> Groupname: SBT First atomname: SBT First atomnr 761
>> Groupname: OBT First atomname: OBT First atomnr 763
>> Groupname: CBT First atomname: CBT First atomnr 764
>> Groupname: F1 First atomname: F1 First atomnr 768
>>
>> Reading frame 0 time 0.000 Number of elements in first group:
>> 10360
>>
>> -------------------------------------------------------
>> Program: gmx order, version 2019.1
>> Source file: src/gromacs/gmxana/gmx_order.cpp (line 546)
>>
>> Fatal error:
>> grp 1 does not have same number of elements as grp 1
>>
>> can anybody help.
>>
>> Thanks
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 2
> Date: Sat, 15 Feb 2020 16:52:13 +0200
> From: Marwa Abd El Kader <ph.marwaabdelkader at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Trajectory optimization - 2 chains are
> separated
> Message-ID:
> <CAJ+3OUZRqUfHUjfFSWu8Xzpg0p7_Bf305meufei0V9mvnUUwJQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear Justin,
> I 've tried centering on one chain and the same problem still exists, any
> suggestions?
>
> On Fri, Feb 14, 2020, 4:01 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 2/14/20 2:48 AM, Marwa Abd El Kader wrote:
>>> Dear Justin,
>>> Would you please tell me how, give me an example code, because I'm a
>> novice?
>>
>> The same thing you did before but instead of trying to select
>> interfacial residues, make an index group of one of the protein chains
>> and select it for the centering group.
>>
>> -Justin
>>
>>> Thanks in advance,
>>> Marwa
>>>
>>> On Fri, Feb 14, 2020, 4:33 AM Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>>
>>>> On 2/13/20 1:33 PM, Marwa Abd El Kader wrote:
>>>>> Dear gmx-users mailing list team,
>>>>> I want to know how to fix the separation of 2 chains after the
>> production
>>>>> run. I'm trying different combinations of trjconv after creating an
>> index
>>>>> file having a specific residue(s) on the interface between the 2
>> chains,
>>>>> but nothing is working. I fixed this issue before but when there was
>> only
>>>>> one chain, now with 2 chains, I don't know how to rejoin them together
>>>>> again. Can you suggest me any solution, please?!
>>>>> *N.B: the 2 chains are considered as one when selected in VMD
>>>> Center on a single chain rather than trying to work with the interface
>>>> residues.
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Assistant Professor
>>>> Office: 301 Fralin Hall
>>>> Lab: 303 Engel Hall
>>>>
>>>> Virginia Tech Department of Biochemistry
>>>> 340 West Campus Dr.
>>>> Blacksburg, VA 24061
>>>>
>>>> jalemkul at vt.edu | (540) 231-3129
>>>> http://www.thelemkullab.com
>>>>
>>>> ==================================================
>>>>
>>>> --
>>>> 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-request at gromacs.org.
>>>>
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
>> --
>> 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-request at gromacs.org.
>>
>
>
> ------------------------------
>
> Message: 3
> Date: Sat, 15 Feb 2020 21:11:20 +0530
> From: Devargya Chakraborty <devargyachakraborty.kgp at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] problem while calculating order parameter
> Message-ID:
> <CAJMw3wjq32jLpCZoXhvC4P6m5StrCOK5aLA7tBXHxx5=1iahKg at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Thanks
>
> On Sat, Feb 15, 2020, 8:02 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 2/15/20 4:50 AM, Devargya Chakraborty wrote:
>>> i want to calculate the order prameter between two carbon atom namrd C01
>>> and C03 in my topology file but while calculating, i am getting the
>>> following error.
>>
>> gmx order is designed to compute deuterium order parameters in alkyl
>> chains. It requires special index groups that only contain the atoms of
>> interest and those flanking them to define the local molecular axis. See
>> http://www.mdtutorials.com/gmx/membrane_protein/09_analysis.html for an
>> example.
>>
>> -Justin
>>
>>> Taking z axis as normal to the membrane
>>> Reading file nvt.tpr, VERSION 2019.1 (single precision)
>>> Using following groups:
>>> Groupname: System First atomname: C01 First atomnr 0
>>> Groupname: Other First atomname: C01 First atomnr 0
>>> Groupname: EMI First atomname: C01 First atomnr 0
>>> Groupname: NSC First atomname: NBT First atomnr 760
>>> Groupname: Water First atomname: OW First atomnr 1360
>>> Groupname: SOL First atomname: OW First atomnr 1360
>>> Groupname: non-Water First atomname: C01 First atomnr 0
>>> Groupname: C01 First atomname: C01 First atomnr 0
>>> Groupname: C04 First atomname: C04 First atomnr 1
>>> Groupname: C03 First atomname: C03 First atomnr 2
>>> Groupname: H07 First atomname: H07 First atomnr 3
>>> Groupname: H09 First atomname: H09 First atomnr 4
>>> Groupname: H08 First atomname: H08 First atomnr 5
>>> Groupname: C05 First atomname: C05 First atomnr 6
>>> Groupname: H0B First atomname: H0B First atomnr 7
>>> Groupname: H0C First atomname: H0C First atomnr 8
>>> Groupname: H0D First atomname: H0D First atomnr 9
>>> Groupname: N00 First atomname: N00 First atomnr 10
>>> Groupname: C06 First atomname: C06 First atomnr 11
>>> Groupname: H0F First atomname: H0F First atomnr 12
>>> Groupname: C0N First atomname: C0N First atomnr 13
>>> Groupname: H0O First atomname: H0O First atomnr 14
>>> Groupname: H0P First atomname: H0P First atomnr 15
>>> Groupname: H0Q First atomname: H0Q First atomnr 16
>>> Groupname: N02 First atomname: N02 First atomnr 17
>>> Groupname: H0E First atomname: H0E First atomnr 18
>>> Groupname: NBT First atomname: NBT First atomnr 760
>>> Groupname: SBT First atomname: SBT First atomnr 761
>>> Groupname: OBT First atomname: OBT First atomnr 763
>>> Groupname: CBT First atomname: CBT First atomnr 764
>>> Groupname: F1 First atomname: F1 First atomnr 768
>>>
>>> Reading frame 0 time 0.000 Number of elements in first group:
>>> 10360
>>>
>>> -------------------------------------------------------
>>> Program: gmx order, version 2019.1
>>> Source file: src/gromacs/gmxana/gmx_order.cpp (line 546)
>>>
>>> Fatal error:
>>> grp 1 does not have same number of elements as grp 1
>>>
>>> can anybody help.
>>>
>>> Thanks
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
>> --
>> 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-request at gromacs.org.
>>
>
>
> ------------------------------
>
> Message: 4
> Date: Sat, 15 Feb 2020 11:12:47 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Trajectory optimization - 2 chains are
> separated
> Message-ID: <840fe62c-e72c-2c59-b6d5-24d07f7e1543 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 2/15/20 9:52 AM, Marwa Abd El Kader wrote:
>> Dear Justin,
>> I 've tried centering on one chain and the same problem still exists, any
>> suggestions?
>
> If centering on one chain via trjconv -center -pbc mol does not yield
> dimers, then I suspect the two chains are not actually associated and
> what you're observing is not actually a PBC issue, unless your box is
> too small and PBC jumps are unavoidable even if one species is properly
> centered.
>
> -Justin
>
>> On Fri, Feb 14, 2020, 4:01 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>>
>>> On 2/14/20 2:48 AM, Marwa Abd El Kader wrote:
>>>> Dear Justin,
>>>> Would you please tell me how, give me an example code, because I'm a
>>> novice?
>>>
>>> The same thing you did before but instead of trying to select
>>> interfacial residues, make an index group of one of the protein chains
>>> and select it for the centering group.
>>>
>>> -Justin
>>>
>>>> Thanks in advance,
>>>> Marwa
>>>>
>>>> On Fri, Feb 14, 2020, 4:33 AM Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>>> On 2/13/20 1:33 PM, Marwa Abd El Kader wrote:
>>>>>> Dear gmx-users mailing list team,
>>>>>> I want to know how to fix the separation of 2 chains after the
>>> production
>>>>>> run. I'm trying different combinations of trjconv after creating an
>>> index
>>>>>> file having a specific residue(s) on the interface between the 2
>>> chains,
>>>>>> but nothing is working. I fixed this issue before but when there was
>>> only
>>>>>> one chain, now with 2 chains, I don't know how to rejoin them together
>>>>>> again. Can you suggest me any solution, please?!
>>>>>> *N.B: the 2 chains are considered as one when selected in VMD
>>>>> Center on a single chain rather than trying to work with the interface
>>>>> residues.
>>>>>
>>>>> -Justin
>>>>>
>>>>> --
>>>>> ==================================================
>>>>>
>>>>> Justin A. Lemkul, Ph.D.
>>>>> Assistant Professor
>>>>> Office: 301 Fralin Hall
>>>>> Lab: 303 Engel Hall
>>>>>
>>>>> Virginia Tech Department of Biochemistry
>>>>> 340 West Campus Dr.
>>>>> Blacksburg, VA 24061
>>>>>
>>>>> jalemkul at vt.edu | (540) 231-3129
>>>>> http://www.thelemkullab.com
>>>>>
>>>>> ==================================================
>>>>>
>>>>> --
>>>>> 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-request at gromacs.org.
>>>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Office: 301 Fralin Hall
>>> Lab: 303 Engel Hall
>>>
>>> Virginia Tech Department of Biochemistry
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalemkul at vt.edu | (540) 231-3129
>>> http://www.thelemkullab.com
>>>
>>> ==================================================
>>>
>>> --
>>> 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-request at gromacs.org.
>>>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 5
> Date: Sat, 15 Feb 2020 16:44:36 +0000
> From: Neena Susan Eappen <neena.susaneappen at mail.utoronto.ca>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] Script for looping n simulations
> Message-ID:
> <YT1PR01MB3723DA20FCB9231B281B6B65CD140 at YT1PR01MB3723.CANPRD01.PROD.OUTLOOK.COM>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello gromacs users,
>
> I was wondering how to write a script to repeat a simulation (equilibration and production) n times, with each cycle starting with structure from the end of previous cycle.
>
> Many thanks,
> Neena
>
>
> ------------------------------
>
> --
> 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-request at gromacs.org.
>
> End of gromacs.org_gmx-users Digest, Vol 190, Issue 31
> ******************************************************
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