Re: [gmx-users] Problem with PME in LIE

2013-07-17 Thread Justin Lemkul 



On 7/17/13 10:54 AM, Sainitin Donakonda wrote:

I started MD very recently dont have much experience you said i would need
.tpr file which doesnot use PME ? how can i get that ?



By writing a new .mdp file that doesn't use PME.  Please refer to previous 
discussions on this topic.  People ask about LIE frequently, and for some reason 
there seems to be a rash of interest lately...


-Justin


Thanks,
Nitin


On Wed, Jul 17, 2013 at 4:46 PM, Justin Lemkul  wrote:




On 7/17/13 10:43 AM, Sainitin Donakonda wrote:


Ok..thanks...so i will use -rerun option in final production ..step..as
follows...actually i ran 20 ns MD simulation so i used extend option to
run
everything in cluster in correct time

#first 10 ns

grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
MD_10.tpr

mdrun -s MD_10.tpr *-rerun MD_20* -deffnm MD_10


#extension for 10 more ns

tpbconv -s MD_first10.tpr -extend 1 -o md_extended_2.tpr

   mdrun -s md_extended_2.tpr -deffnm MD_second10 *-rerun MD_second10* -cpi

MD_first10.cpt -np 32

Can you please tell is this commands are appropriate for production run
using -rerun option...in help manual it is mentioned that "Neighbor



You will need a new .tpr file that does not use PME.  Then, I would
suggest concatenating the existing .xtc files to streamline the process.  I
also do not recall whether the -rerun option works in parallel, but in any
case it is reasonably fast even in serial.  Thus:

mdrun -s newtpr.tpr -rerun full20ns.xtc


  searching will be performed for every frame, unless nstlist is zero"..

should i set nslist to zero in MDP file?



No.  You want the neighbor list to be updated at every frame in the .xtc,
otherwise you will miss interactions and the output will likely be flawed.

-Justin

  Thanks



On Wed, Jul 17, 2013 at 4:21 PM, Justin Lemkul  wrote:




On 7/17/13 10:12 AM, Sainitin Donakonda wrote:

  Usually i collect data after final production run...after this i take

.xtc
file and analyze it using various gromacs tools ..


  And there you have it.  LIE is just an analysis method like anything

else.
There is no purpose in my mind in reanalyzing nonbonded energies during
equilibration.

-Justin

   thanks,


nitin


On Wed, Jul 17, 2013 at 3:51 PM, Justin Lemkul  wrote:




On 7/17/13 9:21 AM, Sainitin Donakonda wrote:

   Hi justin,



Thanks for explaination .. i already ran MD for both  ligand alone and
protein ligand complex..

So now can you please tell me where should use mdrun -rerun option ..i
mean
at which stage ..should i used in Energy miniminimzation or NVT and
NPT
equilibration or Production run ..

Or should i use mdrun -rerun option at every stage ...? or it should
be
used only at final production run?


   Which simulation stage do you normally use to collect data?



-Justin

Thanks,

  Nitin




On Wed, Jul 17, 2013 at 2:59 PM, Justin Lemkul 
wrote:



  On 7/17/13 8:54 AM, Sainitin Donakonda wrote:


Hi ,



I want to use g_lie for my protein-drug complex to get binding
energy
..i
read some information that we need take care some issues if we used
PME
electrostatics..

Indeed i have used PME in my simulation..

Can any body explain which parameters to be taken care while running
g_LIE
and what is the isssue with PME ..


The long-range mesh terms are not decomposable in a pairwise
manner.

 LIE

assumes that all of your interactions can be broken down from
additive
terms, and this is not the case with PME.


 and why we should use -rerun option beofre running LIE




If you evaluate the energies from a PME simulation, the result
will
be

  off.  If you use plain cutoffs for the dynamics, the simulation

will
probably be junk. So one solution is to run the simulation with PME
to
get
reasonable dynamics, then post-process via mdrun -rerun while
evaluating
energies with plain cutoffs (which one would usually increase beyond
normal
values, IIRC, but I do not use LIE myself).

-Justin

--
==




Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul@outerbanks.umaryland.edu http://umaryland.edu>




| (410)
706-7441

==



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Re: [gmx-users] Problem with PME in LIE

2013-07-17 Thread Sainitin Donakonda 
I started MD very recently dont have much experience you said i would need
.tpr file which doesnot use PME ? how can i get that ?

Thanks,
Nitin


On Wed, Jul 17, 2013 at 4:46 PM, Justin Lemkul  wrote:

>
>
> On 7/17/13 10:43 AM, Sainitin Donakonda wrote:
>
>> Ok..thanks...so i will use -rerun option in final production ..step..as
>> follows...actually i ran 20 ns MD simulation so i used extend option to
>> run
>> everything in cluster in correct time
>>
>> #first 10 ns
>>
>> grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
>> MD_10.tpr
>>
>> mdrun -s MD_10.tpr *-rerun MD_20* -deffnm MD_10
>>
>>
>> #extension for 10 more ns
>>
>> tpbconv -s MD_first10.tpr -extend 1 -o md_extended_2.tpr
>>
>>   mdrun -s md_extended_2.tpr -deffnm MD_second10 *-rerun MD_second10* -cpi
>>
>> MD_first10.cpt -np 32
>>
>> Can you please tell is this commands are appropriate for production run
>> using -rerun option...in help manual it is mentioned that "Neighbor
>>
>
> You will need a new .tpr file that does not use PME.  Then, I would
> suggest concatenating the existing .xtc files to streamline the process.  I
> also do not recall whether the -rerun option works in parallel, but in any
> case it is reasonably fast even in serial.  Thus:
>
> mdrun -s newtpr.tpr -rerun full20ns.xtc
>
>
>  searching will be performed for every frame, unless nstlist is zero"..
>> should i set nslist to zero in MDP file?
>>
>>
> No.  You want the neighbor list to be updated at every frame in the .xtc,
> otherwise you will miss interactions and the output will likely be flawed.
>
> -Justin
>
>  Thanks
>>
>>
>> On Wed, Jul 17, 2013 at 4:21 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 7/17/13 10:12 AM, Sainitin Donakonda wrote:
>>>
>>>  Usually i collect data after final production run...after this i take
 .xtc
 file and analyze it using various gromacs tools ..


  And there you have it.  LIE is just an analysis method like anything
>>> else.
>>> There is no purpose in my mind in reanalyzing nonbonded energies during
>>> equilibration.
>>>
>>> -Justin
>>>
>>>   thanks,
>>>
 nitin


 On Wed, Jul 17, 2013 at 3:51 PM, Justin Lemkul  wrote:



> On 7/17/13 9:21 AM, Sainitin Donakonda wrote:
>
>   Hi justin,
>
>>
>> Thanks for explaination .. i already ran MD for both  ligand alone and
>> protein ligand complex..
>>
>> So now can you please tell me where should use mdrun -rerun option ..i
>> mean
>> at which stage ..should i used in Energy miniminimzation or NVT and
>> NPT
>> equilibration or Production run ..
>>
>> Or should i use mdrun -rerun option at every stage ...? or it should
>> be
>> used only at final production run?
>>
>>
>>   Which simulation stage do you normally use to collect data?
>>
>
> -Justin
>
>Thanks,
>
>  Nitin
>>
>>
>>
>> On Wed, Jul 17, 2013 at 2:59 PM, Justin Lemkul 
>> wrote:
>>
>>
>>
>>  On 7/17/13 8:54 AM, Sainitin Donakonda wrote:
>>>
>>>Hi ,
>>>
>>>
 I want to use g_lie for my protein-drug complex to get binding
 energy
 ..i
 read some information that we need take care some issues if we used
 PME
 electrostatics..

 Indeed i have used PME in my simulation..

 Can any body explain which parameters to be taken care while running
 g_LIE
 and what is the isssue with PME ..


The long-range mesh terms are not decomposable in a pairwise
 manner.

 LIE
>>> assumes that all of your interactions can be broken down from
>>> additive
>>> terms, and this is not the case with PME.
>>>
>>>
>>> and why we should use -rerun option beofre running LIE
>>>
>>>
>>>
If you evaluate the energies from a PME simulation, the result
 will
 be

  off.  If you use plain cutoffs for the dynamics, the simulation
>>> will
>>> probably be junk. So one solution is to run the simulation with PME
>>> to
>>> get
>>> reasonable dynamics, then post-process via mdrun -rerun while
>>> evaluating
>>> energies with plain cutoffs (which one would usually increase beyond
>>> normal
>>> values, IIRC, but I do not use LIE myself).
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>>
>>>
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul@outerbanks.umaryland.edu >> umaryland.edu 
>>> http://umaryland.edu>
>>> 
>>> >>>
>

Re: [gmx-users] Problem with PME in LIE

2013-07-17 Thread Sainitin Donakonda 
Ok..thanks...so i will use -rerun option in final production ..step..as
follows...actually i ran 20 ns MD simulation so i used extend option to run
everything in cluster in correct time

#first 10 ns

grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
MD_10.tpr

mdrun -s MD_10.tpr *-rerun MD_20* -deffnm MD_10

#extension for 10 more ns

tpbconv -s MD_first10.tpr -extend 1 -o md_extended_2.tpr

 mdrun -s md_extended_2.tpr -deffnm MD_second10 *-rerun MD_second10* -cpi
MD_first10.cpt -np 32

Can you please tell is this commands are appropriate for production run
using -rerun option...in help manual it is mentioned that "Neighbor
searching will be performed for every frame, unless nstlist is zero"..
should i set nslist to zero in MDP file?

Thanks


On Wed, Jul 17, 2013 at 4:21 PM, Justin Lemkul  wrote:

>
>
> On 7/17/13 10:12 AM, Sainitin Donakonda wrote:
>
>> Usually i collect data after final production run...after this i take .xtc
>> file and analyze it using various gromacs tools ..
>>
>>
> And there you have it.  LIE is just an analysis method like anything else.
> There is no purpose in my mind in reanalyzing nonbonded energies during
> equilibration.
>
> -Justin
>
>  thanks,
>> nitin
>>
>>
>> On Wed, Jul 17, 2013 at 3:51 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 7/17/13 9:21 AM, Sainitin Donakonda wrote:
>>>
>>>  Hi justin,

 Thanks for explaination .. i already ran MD for both  ligand alone and
 protein ligand complex..

 So now can you please tell me where should use mdrun -rerun option ..i
 mean
 at which stage ..should i used in Energy miniminimzation or NVT and NPT
 equilibration or Production run ..

 Or should i use mdrun -rerun option at every stage ...? or it should be
 used only at final production run?


  Which simulation stage do you normally use to collect data?
>>>
>>> -Justin
>>>
>>>   Thanks,
>>>
 Nitin



 On Wed, Jul 17, 2013 at 2:59 PM, Justin Lemkul  wrote:



> On 7/17/13 8:54 AM, Sainitin Donakonda wrote:
>
>   Hi ,
>
>>
>> I want to use g_lie for my protein-drug complex to get binding energy
>> ..i
>> read some information that we need take care some issues if we used
>> PME
>> electrostatics..
>>
>> Indeed i have used PME in my simulation..
>>
>> Can any body explain which parameters to be taken care while running
>> g_LIE
>> and what is the isssue with PME ..
>>
>>
>>   The long-range mesh terms are not decomposable in a pairwise manner.
>>
>   LIE
> assumes that all of your interactions can be broken down from additive
> terms, and this is not the case with PME.
>
>
>and why we should use -rerun option beofre running LIE
>
>
>>
>>   If you evaluate the energies from a PME simulation, the result will
>> be
>>
> off.  If you use plain cutoffs for the dynamics, the simulation will
> probably be junk. So one solution is to run the simulation with PME to
> get
> reasonable dynamics, then post-process via mdrun -rerun while
> evaluating
> energies with plain cutoffs (which one would usually increase beyond
> normal
> values, IIRC, but I do not use LIE myself).
>
> -Justin
>
> --
> ==**
>
>
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.**edu  umaryland.edu 
> >>
> | (410)
> 706-7441
>
> ==**
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> http://lists.gromacs.org/**mailman/listinfo/gmx-users>
> >
> http://lists.gromacs.org/mailman/**listinfo/gmx-users>
> http://lists.gromacs.org/mailman/listinfo/gmx-users>
> >
>
>
>>  * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<**h**ttp://www.gromacs.org/**Support/**
>
> Mailing_Lists/Search 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-requ...@gromacs.org.
> * Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>

Re: [gmx-users] Problem with PME in LIE

2013-07-17 Thread Justin Lemkul 



On 7/17/13 10:43 AM, Sainitin Donakonda wrote:

Ok..thanks...so i will use -rerun option in final production ..step..as
follows...actually i ran 20 ns MD simulation so i used extend option to run
everything in cluster in correct time

#first 10 ns

grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
MD_10.tpr

mdrun -s MD_10.tpr *-rerun MD_20* -deffnm MD_10

#extension for 10 more ns

tpbconv -s MD_first10.tpr -extend 1 -o md_extended_2.tpr

  mdrun -s md_extended_2.tpr -deffnm MD_second10 *-rerun MD_second10* -cpi
MD_first10.cpt -np 32

Can you please tell is this commands are appropriate for production run
using -rerun option...in help manual it is mentioned that "Neighbor


You will need a new .tpr file that does not use PME.  Then, I would suggest 
concatenating the existing .xtc files to streamline the process.  I also do not 
recall whether the -rerun option works in parallel, but in any case it is 
reasonably fast even in serial.  Thus:


mdrun -s newtpr.tpr -rerun full20ns.xtc


searching will be performed for every frame, unless nstlist is zero"..
should i set nslist to zero in MDP file?



No.  You want the neighbor list to be updated at every frame in the .xtc, 
otherwise you will miss interactions and the output will likely be flawed.


-Justin


Thanks


On Wed, Jul 17, 2013 at 4:21 PM, Justin Lemkul  wrote:




On 7/17/13 10:12 AM, Sainitin Donakonda wrote:


Usually i collect data after final production run...after this i take .xtc
file and analyze it using various gromacs tools ..



And there you have it.  LIE is just an analysis method like anything else.
There is no purpose in my mind in reanalyzing nonbonded energies during
equilibration.

-Justin

  thanks,

nitin


On Wed, Jul 17, 2013 at 3:51 PM, Justin Lemkul  wrote:




On 7/17/13 9:21 AM, Sainitin Donakonda wrote:

  Hi justin,


Thanks for explaination .. i already ran MD for both  ligand alone and
protein ligand complex..

So now can you please tell me where should use mdrun -rerun option ..i
mean
at which stage ..should i used in Energy miniminimzation or NVT and NPT
equilibration or Production run ..

Or should i use mdrun -rerun option at every stage ...? or it should be
used only at final production run?


  Which simulation stage do you normally use to collect data?


-Justin

   Thanks,


Nitin



On Wed, Jul 17, 2013 at 2:59 PM, Justin Lemkul  wrote:




On 7/17/13 8:54 AM, Sainitin Donakonda wrote:

   Hi ,



I want to use g_lie for my protein-drug complex to get binding energy
..i
read some information that we need take care some issues if we used
PME
electrostatics..

Indeed i have used PME in my simulation..

Can any body explain which parameters to be taken care while running
g_LIE
and what is the isssue with PME ..


   The long-range mesh terms are not decomposable in a pairwise manner.


   LIE
assumes that all of your interactions can be broken down from additive
terms, and this is not the case with PME.


and why we should use -rerun option beofre running LIE




   If you evaluate the energies from a PME simulation, the result will
be


off.  If you use plain cutoffs for the dynamics, the simulation will
probably be junk. So one solution is to run the simulation with PME to
get
reasonable dynamics, then post-process via mdrun -rerun while
evaluating
energies with plain cutoffs (which one would usually increase beyond
normal
values, IIRC, but I do not use LIE myself).

-Justin

--
==**



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul@outerbanks.umaryland.**edu >>
| (410)
706-7441

==**


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Re: [gmx-users] Problem with PME in LIE

2013-07-17 Thread Justin Lemkul 



On 7/17/13 10:12 AM, Sainitin Donakonda wrote:

Usually i collect data after final production run...after this i take .xtc
file and analyze it using various gromacs tools ..



And there you have it.  LIE is just an analysis method like anything else. 
There is no purpose in my mind in reanalyzing nonbonded energies during 
equilibration.


-Justin


thanks,
nitin


On Wed, Jul 17, 2013 at 3:51 PM, Justin Lemkul  wrote:




On 7/17/13 9:21 AM, Sainitin Donakonda wrote:


Hi justin,

Thanks for explaination .. i already ran MD for both  ligand alone and
protein ligand complex..

So now can you please tell me where should use mdrun -rerun option ..i
mean
at which stage ..should i used in Energy miniminimzation or NVT and NPT
equilibration or Production run ..

Or should i use mdrun -rerun option at every stage ...? or it should be
used only at final production run?



Which simulation stage do you normally use to collect data?

-Justin

  Thanks,

Nitin



On Wed, Jul 17, 2013 at 2:59 PM, Justin Lemkul  wrote:




On 7/17/13 8:54 AM, Sainitin Donakonda wrote:

  Hi ,


I want to use g_lie for my protein-drug complex to get binding energy
..i
read some information that we need take care some issues if we used PME
electrostatics..

Indeed i have used PME in my simulation..

Can any body explain which parameters to be taken care while running
g_LIE
and what is the isssue with PME ..


  The long-range mesh terms are not decomposable in a pairwise manner.

  LIE
assumes that all of your interactions can be broken down from additive
terms, and this is not the case with PME.


   and why we should use -rerun option beofre running LIE




  If you evaluate the energies from a PME simulation, the result will be

off.  If you use plain cutoffs for the dynamics, the simulation will
probably be junk. So one solution is to run the simulation with PME to
get
reasonable dynamics, then post-process via mdrun -rerun while evaluating
energies with plain cutoffs (which one would usually increase beyond
normal
values, IIRC, but I do not use LIE myself).

-Justin

--
==


Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul@outerbanks.umaryland.edu > | (410)
706-7441

==

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--
==**

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul@outerbanks.umaryland.**edu  | (410)
706-7441

==**
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==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] Problem with PME in LIE

2013-07-17 Thread Sainitin Donakonda 
Usually i collect data after final production run...after this i take .xtc
file and analyze it using various gromacs tools ..

thanks,
nitin


On Wed, Jul 17, 2013 at 3:51 PM, Justin Lemkul  wrote:

>
>
> On 7/17/13 9:21 AM, Sainitin Donakonda wrote:
>
>> Hi justin,
>>
>> Thanks for explaination .. i already ran MD for both  ligand alone and
>> protein ligand complex..
>>
>> So now can you please tell me where should use mdrun -rerun option ..i
>> mean
>> at which stage ..should i used in Energy miniminimzation or NVT and NPT
>> equilibration or Production run ..
>>
>> Or should i use mdrun -rerun option at every stage ...? or it should be
>> used only at final production run?
>>
>>
> Which simulation stage do you normally use to collect data?
>
> -Justin
>
>  Thanks,
>> Nitin
>>
>>
>>
>> On Wed, Jul 17, 2013 at 2:59 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 7/17/13 8:54 AM, Sainitin Donakonda wrote:
>>>
>>>  Hi ,

 I want to use g_lie for my protein-drug complex to get binding energy
 ..i
 read some information that we need take care some issues if we used PME
 electrostatics..

 Indeed i have used PME in my simulation..

 Can any body explain which parameters to be taken care while running
 g_LIE
 and what is the isssue with PME ..


  The long-range mesh terms are not decomposable in a pairwise manner.
>>>  LIE
>>> assumes that all of your interactions can be broken down from additive
>>> terms, and this is not the case with PME.
>>>
>>>
>>>   and why we should use -rerun option beofre running LIE
>>>


  If you evaluate the energies from a PME simulation, the result will be
>>> off.  If you use plain cutoffs for the dynamics, the simulation will
>>> probably be junk. So one solution is to run the simulation with PME to
>>> get
>>> reasonable dynamics, then post-process via mdrun -rerun while evaluating
>>> energies with plain cutoffs (which one would usually increase beyond
>>> normal
>>> values, IIRC, but I do not use LIE myself).
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul@outerbanks.umaryland.edu >> umaryland.edu > | (410)
>>> 706-7441
>>>
>>> ==
>>>
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>> >
>>> * Please search the archive at http://www.gromacs.org/**
>>> Support/Mailing_Lists/Search>> 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-requ...@gromacs.org.
>>> * Can't post? Read 
>>> http://www.gromacs.org/Support/Mailing_Lists
>>> 
>>> >
>>>
>>>
> --
> ==**
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.**edu  | 
> (410)
> 706-7441
>
> ==**
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read 
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Re: [gmx-users] Problem with PME in LIE

2013-07-17 Thread Justin Lemkul 



On 7/17/13 9:21 AM, Sainitin Donakonda wrote:

Hi justin,

Thanks for explaination .. i already ran MD for both  ligand alone and
protein ligand complex..

So now can you please tell me where should use mdrun -rerun option ..i mean
at which stage ..should i used in Energy miniminimzation or NVT and NPT
equilibration or Production run ..

Or should i use mdrun -rerun option at every stage ...? or it should be
used only at final production run?



Which simulation stage do you normally use to collect data?

-Justin


Thanks,
Nitin



On Wed, Jul 17, 2013 at 2:59 PM, Justin Lemkul  wrote:




On 7/17/13 8:54 AM, Sainitin Donakonda wrote:


Hi ,

I want to use g_lie for my protein-drug complex to get binding energy ..i
read some information that we need take care some issues if we used PME
electrostatics..

Indeed i have used PME in my simulation..

Can any body explain which parameters to be taken care while running g_LIE
and what is the isssue with PME ..



The long-range mesh terms are not decomposable in a pairwise manner.  LIE
assumes that all of your interactions can be broken down from additive
terms, and this is not the case with PME.


  and why we should use -rerun option beofre running LIE




If you evaluate the energies from a PME simulation, the result will be
off.  If you use plain cutoffs for the dynamics, the simulation will
probably be junk. So one solution is to run the simulation with PME to get
reasonable dynamics, then post-process via mdrun -rerun while evaluating
energies with plain cutoffs (which one would usually increase beyond normal
values, IIRC, but I do not use LIE myself).

-Justin

--
==**

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul@outerbanks.umaryland.**edu  | (410)
706-7441

==**
--
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http://lists.gromacs.org/**mailman/listinfo/gmx-users
* Please search the archive at http://www.gromacs.org/**
Support/Mailing_Lists/Searchbefore
 posting!
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interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read 
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--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
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Re: [gmx-users] Problem with PME in LIE

2013-07-17 Thread Sainitin Donakonda 
Hi justin,

Thanks for explaination .. i already ran MD for both  ligand alone and
protein ligand complex..

So now can you please tell me where should use mdrun -rerun option ..i mean
at which stage ..should i used in Energy miniminimzation or NVT and NPT
equilibration or Production run ..

Or should i use mdrun -rerun option at every stage ...? or it should be
used only at final production run?

Thanks,
Nitin



On Wed, Jul 17, 2013 at 2:59 PM, Justin Lemkul  wrote:

>
>
> On 7/17/13 8:54 AM, Sainitin Donakonda wrote:
>
>> Hi ,
>>
>> I want to use g_lie for my protein-drug complex to get binding energy ..i
>> read some information that we need take care some issues if we used PME
>> electrostatics..
>>
>> Indeed i have used PME in my simulation..
>>
>> Can any body explain which parameters to be taken care while running g_LIE
>> and what is the isssue with PME ..
>>
>>
> The long-range mesh terms are not decomposable in a pairwise manner.  LIE
> assumes that all of your interactions can be broken down from additive
> terms, and this is not the case with PME.
>
>
>  and why we should use -rerun option beofre running LIE
>>
>>
> If you evaluate the energies from a PME simulation, the result will be
> off.  If you use plain cutoffs for the dynamics, the simulation will
> probably be junk. So one solution is to run the simulation with PME to get
> reasonable dynamics, then post-process via mdrun -rerun while evaluating
> energies with plain cutoffs (which one would usually increase beyond normal
> values, IIRC, but I do not use LIE myself).
>
> -Justin
>
> --
> ==**
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.**edu  | 
> (410)
> 706-7441
>
> ==**
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>
-- 
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Re: [gmx-users] Problem with PME in LIE

2013-07-17 Thread Justin Lemkul 



On 7/17/13 8:54 AM, Sainitin Donakonda wrote:

Hi ,

I want to use g_lie for my protein-drug complex to get binding energy ..i
read some information that we need take care some issues if we used PME
electrostatics..

Indeed i have used PME in my simulation..

Can any body explain which parameters to be taken care while running g_LIE
and what is the isssue with PME ..



The long-range mesh terms are not decomposable in a pairwise manner.  LIE 
assumes that all of your interactions can be broken down from additive terms, 
and this is not the case with PME.



and why we should use -rerun option beofre running LIE



If you evaluate the energies from a PME simulation, the result will be off.  If 
you use plain cutoffs for the dynamics, the simulation will probably be junk. 
So one solution is to run the simulation with PME to get reasonable dynamics, 
then post-process via mdrun -rerun while evaluating energies with plain cutoffs 
(which one would usually increase beyond normal values, IIRC, but I do not use 
LIE myself).


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
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[gmx-users] Problem with PME in LIE

2013-07-17 Thread Sainitin Donakonda 
Hi ,

I want to use g_lie for my protein-drug complex to get binding energy ..i
read some information that we need take care some issues if we used PME
electrostatics..

Indeed i have used PME in my simulation..

Can any body explain which parameters to be taken care while running g_LIE
and what is the isssue with PME ..

and why we should use -rerun option beofre running LIE

Regards,
Sainitin
-- 
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