[gmx-users] checking simulation time
Bukunmi Akinwunmi
bukunmi.akinwunmi at uef.fi
Wed Oct 4 09:22:06 CEST 2017
thanks Justin and Tasneem. but how do i retrieve the log file from an ongoing simulation. all I have is the job id because I am using a cluster for the calculation.
Best Regards,
Bukunmi
-----Original Message-----
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Today's Topics:
1. Re: peptide ligand (Justin Lemkul)
2. Re: checking simulation progress (Justin Lemkul)
3. Re: checking simulation progress (Tasneem Kausar)
4. Re: gromacs.org_gmx-users Digest, Vol 162, Issue 7
(zaved at tezu.ernet.in)
----------------------------------------------------------------------
Message: 1
Date: Tue, 3 Oct 2017 12:28:48 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] peptide ligand
Message-ID: <c6760a02-054a-939b-1ff0-4eb996086c8c at vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
On 10/3/17 11:13 AM, farial tavakoli wrote:
> blockquote, div.yahoo_quoted { margin-left: 0 !important;
> border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Thanks alot for your advxe I would really appreciate if you advice me more to split protein and ligand in index file, I saw the index help , but couldnt find out how should I use ? ?splitch? nr ? script to split them.
> With best regardsFarial
>
Index files aren't used with pdb2gmx. The splitting functions of make_ndx break a chain down into its component residues. That's not at all what you want to do.
-Justin
>
> Sent from Yahoo Mail for iPhone
>
>
> On Tuesday, October 3, 2017, 4:51 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
> On 10/3/17 9:17 AM, ?farial tavakoli? ? wrote:
>> Dear Justin
>>
>> Thank you so much for your reply.
>> You mean , I should generate a topology file for my complex instead
>> of creating topology for each of them separately ?
>>
>
> As long as the protein and peptide ligand are denoted as being in
> separate chains (different chain ID or use of TER in the PDB file),
> then pdb2gmx will do everything for you.
>
> -Justin
>
>>
>>
>> ---------------------------------------------------------------------
>> ---
>> *From:* Justin Lemkul <jalemkul at vt.edu>
>> *To:* gmx-users at gromacs.org; ?farial tavakoli? ?
>> <farial.tavakoli at ymail.com>
>> *Sent:* Tuesday, 3 October 2017, 16:35:49
>> *Subject:* Re: [gmx-users] peptide ligand
>>
>>
>>
>> On 10/3/17 4:26 AM, ?farial tavakoli? ? wrote:
>>> Dear GROMACS users
>>> I need to run a MD on my Protein-peptide ligand complex in GROMACS.
>> I generated my ligand topology by gromose96 54a7 ff ( [moleculetypes]
>> was Protein_chain_B) and converted it to .itp file to string it in
>> Protein.top file, then, added Protein_chain_B in [ molecules ]
>> directive to create one topology file for my complex. Created newbox
>> and solvate.
>>
>> You shouldn't have to do any topology manipulation. pdb2gmx handles
>> multiple chains natively without any additional effort on your part.
>>
>> -Justin
>>
>>
>>> But when I gave this command:gmx grompp -f em_real.mdp -c
>> solv_ions.gro -p topol.top -o em.tpr
>>>
>>> I faced to this error:
>>>
>>> Group Protein_chain_B referenced in the .mdb 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.
>>>
>>> In spite of , my ligand [ moleculetypes ] in the ligand.itp file is
>> Protein_chain_B , but GROMACS gives error.
>>> Would you please advice me how can I solve this problem?
>>>
>>> Best
>>> Farial
>>
>>>
>>>
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu <mailto:jalemkul at vt.edu> | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>>
>> ==================================================
>>
>>
>
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==================================================
------------------------------
Message: 2
Date: Tue, 3 Oct 2017 12:29:30 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] checking simulation progress
Message-ID: <34c0fcbb-e9c9-f435-f5c8-9c6a7be49db0 at vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed
On 10/3/17 12:03 PM, Bukunmi Akinwunmi wrote:
> dear gmx-users,
> my simulation has been running for sometime but now I want to know how long is left for the simulation to be completed. I need help with the command to analyse a running simulation.
>
The -v option of mdrun prints a running estimate of time remaining, but if you didn't use it then it's no use to you during an ongoing run. Otherwise, just use tail on the .log file to see how far along things are.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==================================================
------------------------------
Message: 3
Date: Tue, 3 Oct 2017 22:07:06 +0530
From: Tasneem Kausar <tasneemkausar12 at gmail.com>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] checking simulation progress
Message-ID:
<CAFaK4UZy6Obns6rey00nUXqtHU2PKHwJNpkV8qV6v1OCGH9FHA at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
see gmx check -h option
On 3 Oct 2017 21:33, "Bukunmi Akinwunmi" <bukunmi.akinwunmi at uef.fi> wrote:
> dear gmx-users,
> my simulation has been running for sometime but now I want to know how
> long is left for the simulation to be completed. I need help with the
> command to analyse a running simulation.
>
> Best regards,
> Bukunmi
> --
> 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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> send a mail to gmx-users-request at gromacs.org.
>
------------------------------
Message: 4
Date: Tue, 3 Oct 2017 22:28:56 +0530
From: zaved at tezu.ernet.in
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 162, Issue
7
Message-ID:
<ea120bd22f3e1c062c42a21b880236f8.squirrel at webmail.tezu.ernet.in>
Content-Type: text/plain;charset=utf-8
> Send gromacs.org_gmx-users mailing list submissions to
> gromacs.org_gmx-users at maillist.sys.kth.se
>
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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> Today's Topics:
>
> 1. Charges and Antechamber (ABEL Stephane)
> 2. Re: peptide ligand (farial tavakoli)
> 3. Re: grompp very slow generating .tpr when excluded bonded
> neighbours is large (Mark Abraham)
> 4. Re: Charges and Antechamber (Jo?o Henriques)
> 5. checking simulation progress (Bukunmi Akinwunmi)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 3 Oct 2017 15:10:33 +0000
> From: ABEL Stephane <Stephane.ABEL at cea.fr>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] Charges and Antechamber
> Message-ID:
> <3E39B768BB199548AB18F7289E7534AF38818043 at EXDAG0-B0.intra.cea.fr>
> Content-Type: text/plain; charset="us-ascii"
>
> HI
>
> It is quite easy to derive RESP charges and use them with GROMACS. You
> could follow the steps
>
> 1) Build a pdb file of your molecule/modified residue
> 2) Use the web server pyRED
> (http://upjv.q4md-forcefieldtools.org/REDServer-Development/) and
> derive the RESP charges. The webserver will also give you all the
> necessary parameters of the ff (mol2 file, atom types, (non)bonded
> parameters)
> 3) Use these parameters to construct a rtp file for GROMACS for a
> given force field
> 4) and finally use pdb2gmx with the pdb file to obtain the itp file.
>
> That's all
>
> Good luck
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 3 Oct 2017 15:13:58 +0000 (UTC)
> From: farial tavakoli <farial.tavakoli at ymail.com>
> To: <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] peptide ligand
> Message-ID: <1201432437.876905.1507043638717 at mail.yahoo.com>
> Content-Type: text/plain; charset=UTF-8
>
> blockquote, div.yahoo_quoted { margin-left: 0 !important;
> border-left:1px #715FFA solid !important; padding-left:1ex !important;
> background-color:white !important; } Thanks alot for your advxe I
> would really appreciate if you advice me more to split protein and
> ligand in index file, I saw the index help , but couldnt find out how
> should I use ? ?splitch? nr ? script to split them.?
> With best regardsFarial
gmx make_ndx -f em.gro -o index.ndx
then select protein ( in your case it will contain both the protein and the peptide) and your ligand.
press q (save it)
now assemble your nvt tpr file using grompp ( pass here -n index.ndx)
It is explained very nicely in gromacs tutorial Protein - Ligand (Equilibration section)
thank you
>
> Sent from Yahoo Mail for iPhone
>
>
> On Tuesday, October 3, 2017, 4:51 PM, Justin Lemkul <jalemkul at vt.edu>
> wrote:
>
>
>
> On 10/3/17 9:17 AM, ?farial tavakoli? ? wrote:
>> Dear Justin
>>
>> Thank you so much for your reply.
>> You mean , I should generate a topology file for my complex instead
>> of creating topology for each of them separately ?
>>
>
> As long as the protein and peptide ligand are denoted as being in
> separate chains (different chain ID or use of TER in the PDB file),
> then pdb2gmx will do everything for you.
>
> -Justin
>
>>
>>
>> ---------------------------------------------------------------------
>> ---
>> *From:* Justin Lemkul <jalemkul at vt.edu>
>> *To:* gmx-users at gromacs.org; ?farial tavakoli? ?
>> <farial.tavakoli at ymail.com>
>> *Sent:* Tuesday, 3 October 2017, 16:35:49
>> *Subject:* Re: [gmx-users] peptide ligand
>>
>>
>>
>> On 10/3/17 4:26 AM, ?farial tavakoli? ? wrote:
>> > Dear GROMACS users
>> > I need to run a MD on my Protein-peptide ligand complex in GROMACS.
>> I generated my ligand topology by gromose96 54a7 ff ( [moleculetypes]
>> was Protein_chain_B) and converted it to .itp file to string it in
>> Protein.top file, then, added Protein_chain_B in [ molecules ]
>> directive to create one topology file for my complex. Created newbox
>> and solvate.
>>
>> You shouldn't have to do any topology manipulation. pdb2gmx handles
>> multiple chains natively without any additional effort on your part.
>>
>> -Justin
>>
>>
>> > But when I gave this command:gmx grompp -f em_real.mdp -c
>> solv_ions.gro -p topol.top -o em.tpr
>> >
>> > I faced to this error:
>> >
>> > Group Protein_chain_B referenced in the .mdb 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.
>> >
>> > In spite of , my ligand [ moleculetypes ] in the ligand.itp file is
>> Protein_chain_B , but GROMACS gives error.
>> > Would you please advice me how can I solve this problem?
>> >
>> > Best
>> > Farial
>>
>> >
>> >
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu <mailto:jalemkul at vt.edu> | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>>
>> ==================================================
>>
>>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
> --
> 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: Tue, 03 Oct 2017 15:37:31 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] grompp very slow generating .tpr when
> excluded bonded neighbours is large
> Message-ID:
> <CAMNuMATwCXNMaXV7wxrHjNH6o-Nz9vKPXVWtO41N+9mi8KJk1Q at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> I'm sure we have opportunities to improve this code - please do file a
> redmine issue with repro inputs so we can profile and see!
>
> Thanks,
>
> Mark
>
> On Tue, Oct 3, 2017 at 3:05 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 10/2/17 11:14 PM, Dallas Warren wrote:
>> > Thanks for the reply Justin.
>> >
>> > I am just going to use the largest exclusion bond distance I can,
>> > then ignore the RDF of those beyond that distance.
>> >
>> > Seems curious to me (not actually understanding what grommp is
>> > generating) that the list is so large. These are linear molecules,
>> > 38 atoms, 60 molecules in total.
>>
>> It generates a matrix of all possible exclusions, sorts them, then
>> removes duplicates. So for nrexcl = 37 you need memory on the order
>> of 37 * 37 *
>> 60 * (2
>> * sizeof(int)) - the factor of 2 for the atom numbers comes from the
>> fact that you're actually allocating an array of type "sortable"
>> which is a pair of atom numbers.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>> --
>> 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: Tue, 3 Oct 2017 17:41:27 +0200
> From: Jo?o Henriques <joao.m.a.henriques at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Charges and Antechamber
> Message-ID:
> <CAHv45qPTFJMwRjoXxBYU-EGxU6toR2ZmZWq=7eQ14gC9v_A0pQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Or this... :) I've never used it, but I'm sure it works like a charm.
> I personally prefer to be more involved in all stages of the process,
> but I'm a bit old school and I like to avoid "black boxes" for my own
> learning benefit. That being said, I'm sure it does the job and it's
> faster & simpler. It's probably the best way to go for someone with
> less experience with this sort of task.
>
> Cheers,
>
> J
>
> On Oct 3, 2017 5:10 PM, "ABEL Stephane" <Stephane.ABEL at cea.fr> wrote:
>
> HI
>
> It is quite easy to derive RESP charges and use them with GROMACS. You
> could follow the steps
>
> 1) Build a pdb file of your molecule/modified residue
> 2) Use the web server pyRED (http://upjv.q4md-
> forcefieldtools.org/REDServer-Development/) and derive the RESP charges.
> The webserver will also give you all the necessary parameters of the
> ff
> (mol2 file, atom types, (non)bonded parameters)
> 3) Use these parameters to construct a rtp file for GROMACS for a
> given force field
> 4) and finally use pdb2gmx with the pdb file to obtain the itp file.
>
> That's all
>
> Good luck
> --
> 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: 5
> Date: Tue, 3 Oct 2017 16:03:01 +0000
> From: Bukunmi Akinwunmi <bukunmi.akinwunmi at uef.fi>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] checking simulation progress
> Message-ID:
>
> <HE1PR01MB2940456C37826A4807AAAE1385720 at HE1PR01MB2940.eurprd01.prod.ex
> changelabs.com>
>
> Content-Type: text/plain; charset="us-ascii"
>
> dear gmx-users,
> my simulation has been running for sometime but now I want to know how
> long is left for the simulation to be completed. I need help with the
> command to analyse a running simulation.
>
> Best regards,
> Bukunmi
>
>
> ------------------------------
>
> --
> 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 162, Issue 7
> *****************************************************
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