[gmx-users] Re: crashed simulation: simulation of docked proteins in spc water crashes with LINCS warning (Mark Abraham)
Sanjay Kumar Upadhyay
sanjay23 at iitb.ac.in
Fri Feb 11 11:14:32 CET 2011
--
Regards
Sanjay Kumar Upadhyay
Research Scholor
Protein Dynamics lab
Dept of Chemistry
IIT Powai, Mumbai, 400076
Ph no. 09920200345, 09699353562,
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>Dear Marks
thanks for your suggestion,
Sorry, in previous mail i did not write md protocol in details what i
followed for simulation. after energy minimization steps i did PR for 200
ps and then run the production MD. Even i did vacuum energy minimization
before adding solvent for all systems. I used steep followed by cg for
prot-solvent energy minimization which reached up to minimum applied force
100 KJ/mol/nm.
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> Today's Topics:
>
> 1. Re: crashed simulation: simulation of docked proteins in spc
> water crashes with LINCS warning (Mark Abraham)
> 2. re: extending the simulation (bharat gupta)
> 3. Fwd: Question on Gromacs: rlist, rvdw, rcoulomb
> (David van der Spoel)
> 4. Re: Extending the simulation (bharat gupta)
> 5. Re: PRODRG (mohsen ramezanpour)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 11 Feb 2011 16:59:07 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] crashed simulation: simulation of docked
> proteins in spc water crashes with LINCS warning
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4D54D02B.5030705 at anu.edu.au>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> On 11/02/2011 3:47 PM, Sanjay Kumar Upadhyay wrote:
>>
>> Dear gmx-users
>> I am experiencing some problems running a protein-protein docked
>> structures in water(GROMOS43a1/SPC)with gmx-4.0.4 using 8 CPUs.
>>
>> I have 20 docked (protein-protein) structures of one common protein with
>> two different homologous protein, 10 from each group and started
>> simulations for all, using same parameters.
>>
>> I did energy minimization for all the systems, all systems reached to
>> energy minimized configuration in between 10000 to 12000 steps using
>> steep
>> algorithm and PE for all minimized systems are vary between -3975853 to
>> -3571906 KJ/mol.
>>
>> In final MD out off 10 simulations 9 from each group was crassed in
>> between 200 ps to 900 ps with lincs warning. However one simulation from
>> each group running well up to 5 ns, and after 5ns out of these two, one
>> simulation crassed with too many lincs warning, while other one
>> completed
>> 20ns and steel continue.
>
> It sounds like you are not using a proper equilibration protocol before
> attempting to run MD. Occasionally that can work, but often it doesn't.
> See
> http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
>
> Mark
>
>> when restarting the *crashed *simulation feeding "-cpi md.cpt" to mdrun
>> the simulation restarts fine with few steps before but stopped at same
>> portion of the simulation with same lincs warning. I checked the energy
>> and temperature distribution and find that potential energy is
>> fine,however total energy of systems as well as temperature (300K attain
>> 321K
>> at last steps) is higher at last steps before simulation stops.I read
>> all the mailing least before posting this question but did not reach any
>> conclusion. Any explanation or solution for this, why one simulation is
>> stable and running fine up to more than 20ns however others are crassed
>> with same parameters?? I am thinking that it may be because of steric
>> class between docked protein. Is it mean that one docked structure
>> making
>> more
>> natural interaction in compare to other docked structures???
>>
>>
>> Regards
>> Sanjay Kumar Upadhyay
>> Research Scholor
>> Protein Dynamics lab
>> Dept of Chemistry
>> IIT Powai, Mumbai, 400076
>> Ph no. 09920200345, 09699353562,
>>
>>
>>
>>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 10 Feb 2011 23:41:07 -0800
> From: bharat gupta <bharat.85.monu at gmail.com>
> Subject: [gmx-users] re: extending the simulation
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <AANLkTinze_KZz+GuHKPb3agb87a7UPr3vZ=hQ1WpLVx1 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
> I extended by 3ns simulation by 2 more ns ... i.e total 5 ns but the .xtc
> file shows only the 3ns trajectories and after checking the md.log file ,
> its showing that it completed those 2 ns steps also... then how can I get
> the trajectory for those 2ns ... I used the following commands for
> extending
> the simulation ...
>
> tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
> mdrun -s next.tpr -cpi previous.cpt
>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46010 at yahoo.com
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> ------------------------------
>
> Message: 3
> Date: Fri, 11 Feb 2011 08:55:01 +0100
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: [gmx-users] Fwd: Question on Gromacs: rlist, rvdw, rcoulomb
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc: Qin Qiao <qiaoqin47 at gmail.com>
> Message-ID: <4D54EB55.6080800 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
> I am a user of gromacs. I am quite confused when I came across the
> relation of rlist and rvdw / rcoulomb in vdw and coulomb calculation.
>
> In cut-off, it says rvdw / rcoulomb should be greater than rlist, while
> in switch/shift, it says rvdw should be smaller than rlist...
>
> I guess in cut-off, it's to get all the updated atoms in the calculation
> of vdw/ coulomb by setting rvdw/ rcoulomb greater, but why it's the
> opposite in switch...
>
> Could you help me to understand how it's done? Thanks a lot.
>
> Best,
>
> Qin
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 11 Feb 2011 01:10:54 -0800
> From: bharat gupta <bharat.85.monu at gmail.com>
> Subject: [gmx-users] Re: Extending the simulation
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <AANLkTikrLZpbvgHJXP1Nt0XFCE8B+FsUSSbBt__-rPWv at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
> I extended by 3ns simulation by 2 more ns ... i.e total 5 ns but the .xtc
> file shows only the 3ns trajectories and after checking the md.log file ,
> its showing that it completed those 2 ns steps also... then how can I get
> the trajectory for those 2ns ... I used the following commands for
> extending
> the simulation ...
>
> tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
> mdrun -s next.tpr -cpi previous.cpt
>
>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46010 at yahoo.com
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> ------------------------------
>
> Message: 5
> Date: Fri, 11 Feb 2011 12:48:31 +0330
> From: mohsen ramezanpour <ramezanpour.mohsen at gmail.com>
> Subject: Re: [gmx-users] PRODRG
> To: jalemkul at vt.edu, Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Message-ID:
> <AANLkTikgvakUo2Onxpb2kzrxECCHzVrenb1MJ6+JjzHh at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Dr.Justin
>
> I did it,it works.Thanks.
>
> there are another problem:
> I want to add some hydogens to my topology.
> I used ADDHYD atomname,But this dosen't work.
> PLease let me know how can I include some Hydrogenes in my topology.
> Thanks in advance
> Mohsen
>
> On Thu, Feb 10, 2011 at 7:56 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> mohsen ramezanpour wrote:
>>
>>> Dear Dr.Justin
>>>
>>> I have read this section before.
>>> There are 2 problem:
>>> 1:ADDHYD atomname and DELHYD atomname commands dosen't work!
>>> they result in ERROR in PRODRG
>>>
>>>
>> You have to run PRODRG twice. The first time, you get the wrong output.
>> Note the atom name that PRODRG assigns to your N atom. The second
>> time,
>> use DELHYD (name). If that doesn't work, then I have no idea and you're
>> better off submitting your question to the PRODRG developers.
>>
>>
>> 2:Actually I don't know the additional hydrogen is necessary or not!
>>> Because it may be necessary for proper protonation.
>>> My drug(Sertraline) is in a solvent,it may interact with water
>>> molecules
>>> and Nitrogen may get an additional hydrogen.
>>>
>>>
>> A doubly-protonated secondary amine would be a fairly strong acid. You
>> should do a pKa calculation to determine what is relevant rather than
>> guessing. There are web servers and other software out there that can
>> do
>> this for you. Google is your friend.
>>
>> -Justin
>>
>> What do you think?
>>>
>>>
>>>
>>> On Wed, Feb 9, 2011 at 9:39 PM, Justin A. Lemkul
>>> <jalemkul at vt.edu<mailto:
>>> jalemkul at vt.edu>> wrote:
>>>
>>>
>>> The OP's question is easily answered by referring to the PRODRG FAQ
>>> in dealing with proper protonation.
>>>
>>> As for Antechamber and the like, these are good tools, but do not
>>> produce GROMOS-compatible topologies, if that is indeed the
>>> underlying goal. We've done thorough analysis of various QM
>>> calculation methods for GROMOS charges, and none of them produce
>>> completely satisfactory topologies. Antechamber, Spartan, Gaussian,
>>> etc are good for initial charge calculations, but IMHO do not
>>> qualify as an "end result" for GROMOS parameterization due to the
>>> empirical refinement used in the force field derivation. All of
>>> that makes GROMOS parameterization somewhat tricky, and hence why
>>> force field choice is so incredibly important when designing
>>> projects... ;)
>>>
>>> -Justin
>>>
>>>
>>> TJ Mustard wrote:
>>>
>>>
>>>
>>> Yes I would recommend acpype.
>>>
>>> On February 9, 2011 at 9:42 AM
>>> jorge_quintero at ciencias.uis.edu.co
>>> <mailto:jorge_quintero at ciencias.uis.edu.co> wrote:
>>>
>>> > I think that is better to use antechamber tools.
>>> >
>>> >
>>> > > On 10/02/2011 3:40 AM, mohsen ramezanpour wrote:
>>> > >> Dear Users
>>> > >>
>>> > >> I am using PRODRG to make topology for my drug
>>> > >> It addes Hydrogenes but in wrong way.
>>> > >> My Nitrogen atom is bonded to 2 Carbos,
>>> > >> and PRODRG addes 2 Hydrogenes to it .
>>> > >> Please let me know how can I do.
>>> > >> Thanks in advance
>>> > >
>>> > > This is not really the forum to get help about that. You
>>> need to read
>>> > > how to PRODRG needs input, and supply something it can deal
>>> with. Then
>>> > > do a whole bunch more work testing what it produced.
>>> > >
>>> > > Mark
>>> > > --
>>> > > gmx-users mailing list gmx-users at gromacs.org
>>> <mailto:gmx-users at gromacs.org>
>>>
>>> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> > > Please search the archive at
>>> > > http://www.gromacs.org/Support/Mailing_Lists/Search before
>>> posting!
>>> > > Please don't post (un)subscribe requests to the list. Use
>>> the
>>> > > www interface or send it to gmx-users-request at gromacs.org
>>> <mailto:gmx-users-request at gromacs.org>.
>>>
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>>> http://www.gromacs.org/Support/Mailing_Lists
>>> > >
>>> >
>>> >
>>> > --
>>> > Jorge R. Quintero
>>> > Qu?mico
>>> > Universidad Industrial de Santander
>>> > Bucaramanga, Santander - Colombia
>>> >
>>> > --
>>> > gmx-users mailing list gmx-users at gromacs.org
>>> <mailto:gmx-users at gromacs.org>
>>>
>>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> > Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before
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>>> > Please don't post (un)subscribe requests to the list. Use the
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>>> >
>>>
>>> TJ Mustard
>>> Email: mustardt at onid.orst.edu <mailto:mustardt at onid.orst.edu>
>>>
>>>
>>>
>>> -- ========================================
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> MILES-IGERT Trainee
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>>
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> ========================================
>>> -- gmx-users mailing list gmx-users at gromacs.org
>>> <mailto:gmx-users at gromacs.org>
>>>
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>>>
>>>
>>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> --
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
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>> or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
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