subject:"Re\: \[gmx\-users\] rvdw and rcoulomb"

Re: [gmx-users] rvdw and rcoulomb

2018-03-13 Thread Justin Lemkul




On 3/13/18 7:23 AM, Ahmed Mashaly wrote:

Dear Justin,

What do you mean by incorrect?
I understand it is higher than it should be (0.8 - 1 nm), it will consume more 
time, but won't give wrong results, am I correct?


With PME, the value of rcoulomb becomes somewhat irrelevant, but in 
general, one should *not* deviate from prescribed force field cutoff 
values. Force fields are parametrized under a certain set of 
assumptions. If you then deviate from those assumptions, you potentially 
imbalance forces. The simulation will happily run and potentially 
produce incorrect results.


Find the proper values in primary literature (something everyone should 
do before even deciding on a force field) and use those values. GROMACS 
will tune rcoulomb slightly for PME performance reasons, and this is 
fine, but don't go messing with the stock values haphazardly.


-Justin


Kind Regards,
Ahmed


From: Justin Lemkul <jalem...@vt.edu>
To: gmx-us...@gromacs.org
Sent: Tuesday, March 13, 2018 12:18 PM
Subject: Re: [gmx-users] rvdw and rcoulomb





On 3/13/18 5:17 AM, Ahmed Mashaly wrote:

Thanks guys

It is AMBER ff
Using 1,2 is slowing the calculations, I found it late, can I reduce it to 1 
for continuation with no effect on the results? And if I do the other restarts 
starting from 1 or it will give different results?

You shouldn't switch physical models mid-simulation. Start over using
the correct value (1.2 nm is incorrect for AMBER, anyway).

-Justin


On Mon, 12 Mar, 2018 at 4:37 pm, Szilárd Páll

<pall.szil...@gmail.com> wrote:
Note that rcoulomb, unlike rvdw, when using a PME long-range
electrostatics, is tunable (together with the PME grid spacing).
--
Szilárd


On Mon, Mar 12, 2018 at 3:43 PM, Justin Lemkul <jalem...@vt.edu> wrote:

On 3/11/18 7:33 PM, Ahmed Mashaly wrote:

Dear users,
Can I reduce the rvdw and rcoulomb during MD from 1.2 to 1? Kind
Regards,Ahmed


These values are a function of the force field and are not freely tunable.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==


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--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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Re: [gmx-users] rvdw and rcoulomb

2018-03-13 Thread Ahmed Mashaly

Dear Justin,

What do you mean by incorrect?
I understand it is higher than it should be (0.8 - 1 nm), it will consume more 
time, but won't give wrong results, am I correct? 
Kind Regards,
Ahmed 


From: Justin Lemkul <jalem...@vt.edu>
To: gmx-us...@gromacs.org 
Sent: Tuesday, March 13, 2018 12:18 PM
Subject: Re: [gmx-users] rvdw and rcoulomb





On 3/13/18 5:17 AM, Ahmed Mashaly wrote:
> Thanks guys
>
> It is AMBER ff
> Using 1,2 is slowing the calculations, I found it late, can I reduce it to 1 
> for continuation with no effect on the results? And if I do the other 
> restarts starting from 1 or it will give different results?

You shouldn't switch physical models mid-simulation. Start over using 
the correct value (1.2 nm is incorrect for AMBER, anyway).

-Justin

> On Mon, 12 Mar, 2018 at 4:37 pm, Szilárd Páll
>> <pall.szil...@gmail.com> wrote:
>> Note that rcoulomb, unlike rvdw, when using a PME long-range
>> electrostatics, is tunable (together with the PME grid spacing).
>> --
>> Szilárd
>>
>>
>> On Mon, Mar 12, 2018 at 3:43 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>>>
>>> On 3/11/18 7:33 PM, Ahmed Mashaly wrote:
>>>> Dear users,
>>>> Can I reduce the rvdw and rcoulomb during MD from 1.2 to 1? Kind
>>>> Regards,Ahmed
>>>>
>>> These values are a function of the force field and are not freely tunable.
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalem...@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-requ...@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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>> 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.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] rvdw and rcoulomb

2018-03-13 Thread Justin Lemkul




On 3/13/18 5:17 AM, Ahmed Mashaly wrote:

Thanks guys

It is AMBER ff
Using 1,2 is slowing the calculations, I found it late, can I reduce it to 1 
for continuation with no effect on the results? And if I do the other restarts 
starting from 1 or it will give different results?


You shouldn't switch physical models mid-simulation. Start over using 
the correct value (1.2 nm is incorrect for AMBER, anyway).


-Justin


On Mon, 12 Mar, 2018 at 4:37 pm, Szilárd Páll

 wrote:
Note that rcoulomb, unlike rvdw, when using a PME long-range
electrostatics, is tunable (together with the PME grid spacing).
--
Szilárd


On Mon, Mar 12, 2018 at 3:43 PM, Justin Lemkul  wrote:


On 3/11/18 7:33 PM, Ahmed Mashaly wrote:

Dear users,
Can I reduce the rvdw and rcoulomb during MD from 1.2 to 1? Kind
Regards,Ahmed


These values are a function of the force field and are not freely tunable.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==


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--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] rvdw and rcoulomb

2018-03-13 Thread Ahmed Mashaly

Thanks guys

It is AMBER ff
Using 1,2 is slowing the calculations, I found it late, can I reduce it to 1 
for continuation with no effect on the results? And if I do the other restarts 
starting from 1 or it will give different results?

On Mon, 12 Mar, 2018 at 4:37 pm, Szilárd Páll
> wrote:
>Note that rcoulomb, unlike rvdw, when using a PME long-range
>electrostatics, is tunable (together with the PME grid spacing).
>--
>Szilárd
>
>
>On Mon, Mar 12, 2018 at 3:43 PM, Justin Lemkul  wrote:
>>
>>
>> On 3/11/18 7:33 PM, Ahmed Mashaly wrote:
>>>
>>> Dear users,
>>> Can I reduce the rvdw and rcoulomb during MD from 1.2 to 1? Kind
>>> Regards,Ahmed
>>>
>> These values are a function of the force field and are not freely tunable.
>>
>> -Justin
>>
>> --
>> ==
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalem...@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-requ...@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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>mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] rvdw and rcoulomb

2018-03-12 Thread Szilárd Páll

Note that rcoulomb, unlike rvdw, when using a PME long-range
electrostatics, is tunable (together with the PME grid spacing).
--
Szilárd


On Mon, Mar 12, 2018 at 3:43 PM, Justin Lemkul  wrote:
>
>
> On 3/11/18 7:33 PM, Ahmed Mashaly wrote:
>>
>> Dear users,
>> Can I reduce the rvdw and rcoulomb during MD from 1.2 to 1? Kind
>> Regards,Ahmed
>>
> These values are a function of the force field and are not freely tunable.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@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-requ...@gromacs.org.
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Re: [gmx-users] rvdw and rcoulomb

2018-03-12 Thread Justin Lemkul




On 3/11/18 7:33 PM, Ahmed Mashaly wrote:

Dear users,
Can I reduce the rvdw and rcoulomb during MD from 1.2 to 1? Kind Regards,Ahmed


These values are a function of the force field and are not freely tunable.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] rvdw and rcoulomb

Re: [gmx-users] rvdw and rcoulomb

Re: [gmx-users] rvdw and rcoulomb

Re: [gmx-users] rvdw and rcoulomb

Re: [gmx-users] rvdw and rcoulomb

Re: [gmx-users] rvdw and rcoulomb

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