[gmx-users] Question on gmx editconf, pbc and NPT (Sebastian Muraru)
Sebastian Muraru
sebastian.muraru at grabtop.upb.ro
Thu Dec 27 12:50:00 CET 2018
I think I found a workaround my own problem:
I initially placed everything in a box that includes all present molecules within its borders and solvated it. Then I redefined the box and ran an energy minimisation step.
The em.gro file looks as if everything is solvated fine inside the new box which has molecule_1 at its center.
----- Original Message -----
From: "gromacs org gmx-users-request" <gromacs.org_gmx-users-request at maillist.sys.kth.se>
To: "gromacs org gmx-users" <gromacs.org_gmx-users at maillist.sys.kth.se>
Sent: Thursday, December 27, 2018 1:32:20 PM GMT +02:00 Athens, Beirut, Bucharest, Istanbul
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Today's Topics:
1. Re: how to restart a job in grmacs (spss4 at iacs.res.in)
2. Re: how to restart a job in grmacs (SHAHEE ISLAM)
3. Question on gmx editconf, pbc and NPT (Sebastian Muraru)
4. Re: how to restart a job in grmacs (spss4 at iacs.res.in)
5. Re: how to restart a job in grmacs (SHAHEE ISLAM)
6. electrostatic and LJ energy (Dr Tushar Ranjan Moharana)
----------------------------------------------------------------------
Message: 1
Date: Thu, 27 Dec 2018 16:28:53 +0530
From: spss4 at iacs.res.in
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] how to restart a job in grmacs
Message-ID:
<20181227162853.Horde.xoXxxHF68IvVyQ27yoZ54g1 at mailweb.iacs.res.in>
Content-Type: text/plain; charset=UTF-8; format=flowed; DelSp=Yes
----- Message from SHAHEE ISLAM <islamshahee at gmail.com> ---------
? ? Date: Thu, 27 Dec 2018 16:16:18 +0530
? ? From: SHAHEE ISLAM <islamshahee at gmail.com>
Reply-To: gmx-users at gromacs.org
Subject: [gmx-users] how to restart a job in grmacs
? ? ? To: gmx-users at gromacs.org
> hi,
> i have run a simulation for 10 ns but after 4 ns due to power off the
> job stopped.Then using this gmx mdrun -s md_0_10ns.tpr -cpi
> md_0_10ns.cpt,continue the left simulation.Now after normal
> termination of 10 ns how i wll do the next 5 ns simulation after this
> 10 ns.
> thanking you
> shahee
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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Hi
You can extend the job by generating a new tpr file?
gmx convert-tpr -s old.tpr -extend 5000 -o new.tpr?
then restart the job?
gmx mdrun -s new.tpr -cpi state.cpt
?This will continue the run from 10 ns.
Sunipa
----- End message from SHAHEE ISLAM <islamshahee at gmail.com> -----
------------------------------
Message: 2
Date: Thu, 27 Dec 2018 16:41:21 +0530
From: SHAHEE ISLAM <islamshahee at gmail.com>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] how to restart a job in grmacs
Message-ID:
<CAJZ7aT9yGwciW8TN4hyOG+51QDkY6eqKvpeGAMJygupyW2-PcA at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
thank you so much for your reply.
-extend 5000 what does it signify.if the time step is 2 fs then by
simply multiplying these two it will give 10 ns.
thanking you
On 12/27/18, spss4 at iacs.res.in <spss4 at iacs.res.in> wrote:
> ----- Message from SHAHEE ISLAM <islamshahee at gmail.com> ---------
> ? ? Date: Thu, 27 Dec 2018 16:16:18 +0530
> ? ? From: SHAHEE ISLAM <islamshahee at gmail.com>
> Reply-To: gmx-users at gromacs.org
> Subject: [gmx-users] how to restart a job in grmacs
> ? ? ? To: gmx-users at gromacs.org
>
>> hi,
>> i have run a simulation for 10 ns but after 4 ns due to power off the
>> job stopped.Then using this gmx mdrun -s md_0_10ns.tpr -cpi
>> md_0_10ns.cpt,continue the left simulation.Now after normal
>> termination of 10 ns how i wll do the next 5 ns simulation after this
>> 10 ns.
>> thanking you
>> shahee
>> --
>> 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
>> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>> or send a mail to gmx-users-request at gromacs.org.
>
> Hi
> You can extend the job by generating a new tpr file
> gmx convert-tpr -s old.tpr -extend 5000 -o new.tpr
> then restart the job
> gmx mdrun -s new.tpr -cpi state.cpt
> ?This will continue the run from 10 ns.
> Sunipa
> ----- End message from SHAHEE ISLAM <islamshahee at gmail.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
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> mail to gmx-users-request at gromacs.org.
------------------------------
Message: 3
Date: Thu, 27 Dec 2018 13:12:46 +0200 (EET)
From: Sebastian Muraru <sebastian.muraru at grabtop.upb.ro>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Question on gmx editconf, pbc and NPT
Message-ID:
<1457525096.48541545909166873.JavaMail.root at webmail.chim.upb.ro>
Content-Type: text/plain; charset=utf-8
Hi there! Please help me figure something out.
I have a setup made out of two molecules and I would like to investigate when happens when they meet (graphene + biomolecule). One of them is fixed by position restraints, one of them is mobile. When running a simulation under NPT conditions I assumed pressure is applied so that everything is 'slightly guided' towards the center of the simulation box (given a high enough pressure value). Would that assumption be correct? Or is pressure presumably applied on the faces of the simulation box?
Thus, I figured, since I want to check what happens when the molecules meet, I want molecule_1 to be in the center of the simulation box and have molecule_2 slightly guided towards it. However, given that the distance between the molecules is known and fixed, placing the box so that molecule_1 is at the center leaves a part of molecule_2 out of the box through the top face.
I assumed this would not be a problem during a simulation due to pbc being on, thus allowing the part of molecule_2 that's out of the box to reenter through the bottom layer. However, I also need to go through a solvation step and that I think this complicates things because a part of molecule_2 will not be in solvent. Would you know a workaround for this issue? I try to avoid making the box taller / bigger.
Thanks and a Happy Upcoming New Year to the Gromacs Community!
------------------------------
Message: 4
Date: Thu, 27 Dec 2018 16:47:39 +0530
From: spss4 at iacs.res.in
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] how to restart a job in grmacs
Message-ID:
<20181227164739.Horde.CG717yIbKa2pUA0OtAMywg6 at mailweb.iacs.res.in>
Content-Type: text/plain; charset=UTF-8; format=flowed; DelSp=Yes
----- Message from SHAHEE ISLAM <islamshahee at gmail.com> ---------
? ? Date: Thu, 27 Dec 2018 16:41:21 +0530
? ? From: SHAHEE ISLAM <islamshahee at gmail.com>
Reply-To: gmx-users at gromacs.org
Subject: Re: [gmx-users] how to restart a job in grmacs
? ? ? To: gmx-users at gromacs.org
> thank you so much for your reply.
> -extend 5000 what does it signify.if the time step is 2 fs then by
> simply multiplying these two it will give 10 ns.
> thanking you
>
> On 12/27/18, spss4 at iacs.res.in <spss4 at iacs.res.in> wrote:
>> ----- Message from SHAHEE ISLAM <islamshahee at gmail.com> ---------
>> ? ? Date: Thu, 27 Dec 2018 16:16:18 +0530
>> ? ? From: SHAHEE ISLAM <islamshahee at gmail.com>
>> Reply-To: gmx-users at gromacs.org
>> Subject: [gmx-users] how to restart a job in grmacs
>> ? ? ? To: gmx-users at gromacs.org
>>
>>> hi,
>>> i have run a simulation for 10 ns but after 4 ns due to power off the
>>> job stopped.Then using this gmx mdrun -s md_0_10ns.tpr -cpi
>>> md_0_10ns.cpt,continue the left simulation.Now after normal
>>> termination of 10 ns how i wll do the next 5 ns simulation after this
>>> 10 ns.
>>> thanking you
>>> shahee
>>> --
>>> 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
>>> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>> or send a mail to gmx-users-request at gromacs.org.
>>
>> Hi
>> You can extend the job by generating a new tpr file
>> gmx convert-tpr -s old.tpr -extend 5000 -o new.tpr
>> then restart the job
>> gmx mdrun -s new.tpr -cpi state.cpt
>> ?This will continue the run from 10 ns.
>> Sunipa
>> ----- End message from SHAHEE ISLAM <islamshahee at gmail.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.
>
> --
> 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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Hi
-extend 5000 means you want to extend 5000 ps or 5 ns extra after 10 ns. So
your final trajectory will be for 15 ns.
Sunipa
----- End message from SHAHEE ISLAM <islamshahee at gmail.com> -----
------------------------------
Message: 5
Date: Thu, 27 Dec 2018 16:52:17 +0530
From: SHAHEE ISLAM <islamshahee at gmail.com>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] how to restart a job in grmacs
Message-ID:
<CAJZ7aT_7dCazgSmxA4L_sJ-hKUZHTmBTCQ_03cn8ZiE7MTXrkA at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
thank you
is the trajectory wil be from 0-15 ns or it will be from 10-15 ns.
On 12/27/18, spss4 at iacs.res.in <spss4 at iacs.res.in> wrote:
> ----- Message from SHAHEE ISLAM <islamshahee at gmail.com> ---------
> ? ? Date: Thu, 27 Dec 2018 16:41:21 +0530
> ? ? From: SHAHEE ISLAM <islamshahee at gmail.com>
> Reply-To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] how to restart a job in grmacs
> ? ? ? To: gmx-users at gromacs.org
>
>> thank you so much for your reply.
>> -extend 5000 what does it signify.if the time step is 2 fs then by
>> simply multiplying these two it will give 10 ns.
>> thanking you
>>
>> On 12/27/18, spss4 at iacs.res.in <spss4 at iacs.res.in> wrote:
>>> ----- Message from SHAHEE ISLAM <islamshahee at gmail.com> ---------
>>> ? ? Date: Thu, 27 Dec 2018 16:16:18 +0530
>>> ? ? From: SHAHEE ISLAM <islamshahee at gmail.com>
>>> Reply-To: gmx-users at gromacs.org
>>> Subject: [gmx-users] how to restart a job in grmacs
>>> ? ? ? To: gmx-users at gromacs.org
>>>
>>>> hi,
>>>> i have run a simulation for 10 ns but after 4 ns due to power off the
>>>> job stopped.Then using this gmx mdrun -s md_0_10ns.tpr -cpi
>>>> md_0_10ns.cpt,continue the left simulation.Now after normal
>>>> termination of 10 ns how i wll do the next 5 ns simulation after this
>>>> 10 ns.
>>>> thanking you
>>>> shahee
>>>> --
>>>> 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
>>>> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>>> or send a mail to gmx-users-request at gromacs.org.
>>>
>>> Hi
>>> You can extend the job by generating a new tpr file
>>> gmx convert-tpr -s old.tpr -extend 5000 -o new.tpr
>>> then restart the job
>>> gmx mdrun -s new.tpr -cpi state.cpt
>>> ?This will continue the run from 10 ns.
>>> Sunipa
>>> ----- End message from SHAHEE ISLAM <islamshahee at gmail.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.
>>
>> --
>> 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
>> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>> or send a mail to gmx-users-request at gromacs.org.
>
> Hi
> -extend 5000 means you want to extend 5000 ps or 5 ns extra after 10 ns. So
> your final trajectory will be for 15 ns.
>
> Sunipa
>
> ----- End message from SHAHEE ISLAM <islamshahee at gmail.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: 6
Date: Thu, 27 Dec 2018 17:01:10 +0530
From: Dr Tushar Ranjan Moharana <tusharranjanmoharana at gmail.com>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] electrostatic and LJ energy
Message-ID:
<CAH6CjFgO_HOb8-L4riJStqAib0a2Xaaccm=fzjZbhCSuDhftjQ at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
You can use gmx energy (g_energy). Follow the online manual at
http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-energy.html
Regards
--
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB
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