Re: [gmx-users] high-temperature MD

[OuyangYanhua]

Thank you so much!
> 在 2016年10月7日，上午2:27，Christopher Neale <chris.ne...@alum.utoronto.ca> 写道：
> 
> Depends, actually. There are reasons one might want to simulate a system at 
> 380 K in NVT using the average box volume from the 300 K NPT simulation. 
> Temperature replica exchange typically employs NVT and so might other 
> temperature-based enhanced sampling approaches. Justin's right, you have to 
> think it through, but I'm just chiming in to suggest that the answer is not 
> obvious from this thread thus far. TIP3P water doesn't boil in NPT until 
> somewhere around 550 K, so NPT at 380 K is certainly possible.
> 
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
> <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin 
> Lemkul <jalem...@vt.edu>
> Sent: 06 October 2016 09:34:49
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] high-temperature MD
> 
> On 10/6/16 8:54 AM, OuyangYanhua wrote:
>> Dear Justin,
>>> 
>> I had run a 300K-MD, now I want to run a high-temperature(380K) MD to 
>> compare with the 300K-MD.
>> The 300K is first equilibrated at NVT, then at NPT and production MD at NPT. 
>> So I want to know the high-temperature(380K) MD should run the same as the 
>> 300k, which means the 380k is also first equilibrated at NVT, then at NPT 
>> and production MD at NPT ensemble.
>> 
> 
> Think scientifically.  If you only want to vary the temperature, does it make
> any sense to vary the simulation protocol?
> 
> -Justin
> 
>> Best regards,
>> Ouyang
>> 
>>> 在 2016年10月6日，下午7:22，Justin Lemkul <jalem...@vt.edu> 写道：
>>> 
>>> 
>>> 
>>> On 10/6/16 3:52 AM, YanhuaOuyang wrote:
>>>> Hi, I want to perform a MD of an IDP, whose temperature is set to 380K. As 
>>>> we
>>>> know, the MD is  equilibrated  firstly at NVT,  then at NPT ensemble and
>>>> production MD at NPT ensemble normally. Does someone know whether the 
>>>> 380K-MD
>>>> can only  perform at NVT ensemble since the temperature(380K) is a high
>>>> temperature? Should I run the MD(380K) at NPT ensemble or at NPT ensemble?
>>>> 
>>> 
>>> 380 K is not very high.  What you choose to do needs to be based on 
>>> whatever real-world conditions you want to model.
>>> 
>>> -Justin
>>> 
>>> --
>>> ==
>>> 
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>> 
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>> 
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>> 
>>> ==
>>> --
>>> Gromacs Users mailing list
>>> 
>>> * Please search the archive at 
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>> 
>> 
> 
> --
> ==
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
> ==
> --
> Gromacs Users mailing list
> 
> * Please search the archive at 
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Re: [gmx-users] high-temperature MD

[Christopher Neale]

Depends, actually. There are reasons one might want to simulate a system at 380 
K in NVT using the average box volume from the 300 K NPT simulation. 
Temperature replica exchange typically employs NVT and so might other 
temperature-based enhanced sampling approaches. Justin's right, you have to 
think it through, but I'm just chiming in to suggest that the answer is not 
obvious from this thread thus far. TIP3P water doesn't boil in NPT until 
somewhere around 550 K, so NPT at 380 K is certainly possible.


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul 
<jalem...@vt.edu>
Sent: 06 October 2016 09:34:49
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] high-temperature MD

On 10/6/16 8:54 AM, OuyangYanhua wrote:
> Dear Justin,
>>
> I had run a 300K-MD, now I want to run a high-temperature(380K) MD to compare 
> with the 300K-MD.
> The 300K is first equilibrated at NVT, then at NPT and production MD at NPT. 
> So I want to know the high-temperature(380K) MD should run the same as the 
> 300k, which means the 380k is also first equilibrated at NVT, then at NPT and 
> production MD at NPT ensemble.
>

Think scientifically.  If you only want to vary the temperature, does it make
any sense to vary the simulation protocol?

-Justin

> Best regards,
> Ouyang
>
>> 在 2016年10月6日，下午7:22，Justin Lemkul <jalem...@vt.edu> 写道：
>>
>>
>>
>> On 10/6/16 3:52 AM, YanhuaOuyang wrote:
>>> Hi, I want to perform a MD of an IDP, whose temperature is set to 380K. As 
>>> we
>>> know, the MD is  equilibrated  firstly at NVT,  then at NPT ensemble and
>>> production MD at NPT ensemble normally. Does someone know whether the 
>>> 380K-MD
>>> can only  perform at NVT ensemble since the temperature(380K) is a high
>>> temperature? Should I run the MD(380K) at NPT ensemble or at NPT ensemble?
>>>
>>
>> 380 K is not very high.  What you choose to do needs to be based on whatever 
>> real-world conditions you want to model.
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==
>> --
>> 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-requ...@gromacs.org.
>
>

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] high-temperature MD

[Justin Lemkul]

On 10/6/16 8:54 AM, OuyangYanhua wrote:

Dear Justin,



I had run a 300K-MD, now I want to run a high-temperature(380K) MD to compare 
with the 300K-MD.
The 300K is first equilibrated at NVT, then at NPT and production MD at NPT. So 
I want to know the high-temperature(380K) MD should run the same as the 300k, 
which means the 380k is also first equilibrated at NVT, then at NPT and 
production MD at NPT ensemble.



Think scientifically.  If you only want to vary the temperature, does it make 
any sense to vary the simulation protocol?


-Justin


Best regards,
Ouyang


在 2016年10月6日，下午7:22，Justin Lemkul  写道：



On 10/6/16 3:52 AM, YanhuaOuyang wrote:

Hi, I want to perform a MD of an IDP, whose temperature is set to 380K. As we
know, the MD is  equilibrated  firstly at NVT,  then at NPT ensemble and
production MD at NPT ensemble normally. Does someone know whether the 380K-MD
can only  perform at NVT ensemble since the temperature(380K) is a high
temperature? Should I run the MD(380K) at NPT ensemble or at NPT ensemble?



380 K is not very high.  What you choose to do needs to be based on whatever 
real-world conditions you want to model.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] high-temperature MD

[OuyangYanhua]

Dear Justin,
> 
I had run a 300K-MD, now I want to run a high-temperature(380K) MD to compare 
with the 300K-MD.
The 300K is first equilibrated at NVT, then at NPT and production MD at NPT. So 
I want to know the high-temperature(380K) MD should run the same as the 300k, 
which means the 380k is also first equilibrated at NVT, then at NPT and 
production MD at NPT ensemble.

Best regards,
Ouyang

> 在 2016年10月6日，下午7:22，Justin Lemkul  写道：
> 
> 
> 
> On 10/6/16 3:52 AM, YanhuaOuyang wrote:
>> Hi, I want to perform a MD of an IDP, whose temperature is set to 380K. As we
>> know, the MD is  equilibrated  firstly at NVT,  then at NPT ensemble and
>> production MD at NPT ensemble normally. Does someone know whether the 380K-MD
>> can only  perform at NVT ensemble since the temperature(380K) is a high
>> temperature? Should I run the MD(380K) at NPT ensemble or at NPT ensemble?
>> 
> 
> 380 K is not very high.  What you choose to do needs to be based on whatever 
> real-world conditions you want to model.
> 
> -Justin
> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
> ==
> -- 
> 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
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> mail to gmx-users-requ...@gromacs.org.


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Re: [gmx-users] high-temperature MD

[Justin Lemkul]

On 10/6/16 3:52 AM, YanhuaOuyang wrote:

Hi, I want to perform a MD of an IDP, whose temperature is set to 380K. As we
know, the MD is  equilibrated  firstly at NVT,  then at NPT ensemble and
production MD at NPT ensemble normally. Does someone know whether the 380K-MD
can only  perform at NVT ensemble since the temperature(380K) is a high
temperature? Should I run the MD(380K) at NPT ensemble or at NPT ensemble?



380 K is not very high.  What you choose to do needs to be based on whatever 
real-world conditions you want to model.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] high-temperature MD

[YanhuaOuyang]

Hi,
I want to perform a MD of an IDP, whose temperature is set to 380K. As we know, 
the MD is  equilibrated  firstly at NVT,  then at NPT ensemble and production 
MD at NPT ensemble normally.
Does someone know whether the 380K-MD  can only  perform at NVT ensemble since 
the temperature(380K) is a high temperature?
Should I run the MD(380K) at NPT ensemble or at NPT ensemble?


Best regards,
Ouyang
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