[gmx-users] Varying exchange probabilities between replicas in REMD

[Shubhangi Gupta]

Hello all,

I am trying to do REMD simulation following the methodology
given by Mark Abraham (
http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B).
My system is a small 34 residue protein in explicit water. I have generated
temperatures using the server *http://folding.bmc.uu.se/remd/
*, keeping the exchange probability
constant at 0.2. The smallest temperature is 280K and highest temperature
is 380K. I obtained a total of 20 replicas. However, the log file shows
replica exchange statistics with average exchange probabilities varying
from 0.03 to 0.28. The smaller values are for exchanges between higher
temperature replicas.

I have also tried to reproduce simulations from an old paper which has used
AMBER software, using the temperatures mentioned there. It is for a 35
residue protein in implicit water. The exchange probabilities vary from
0.32 to 0.72 when I am trying this in GROMACS.

As I understand the exchange probabilities should be nearly constant. Can
someone please help me with this. Any help is appreciated.


Regards,
Shubhangi Gupta
PhD Research Scholar (YUS lab)
Dept of Chemistry
Indian Institute of Technology Bombay
Powai, Mumbai-400076.

e-mail ID: ignahbuhs.gup...@gmail.com
   shubhangi_gu...@iitb.ac.in
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[gmx-users] Time series of the number of atoms with the volume

[Mijiddorj B]

Dear GMX users,

I would like to make analysis of atom numbers within the certain volume
such as pore of channel. If you have any experience, please advise me.
How can I use gmx select for this purpose?

Best regards,
Miji
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[gmx-users] topol file inaccessible

[Raag Saluja]

Hi!
I'm simulating a heterodimer. The simulation goes really smoothly till the
MD production step where I get an error saying the topol file is
inaccessible. Can you please help?

Thank you in advance and regards,
Raag
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Re: [gmx-users] (no subject)

[Mark Abraham]

Hi,

Then all you need is the starting point for potential helix formation. You
don't need to see it unravel.

Mark

On Sat, Jul 21, 2018, 05:11 Soham Sarkar  wrote:

> I want to see the helix transition.. whether it is coming back or not in
> the presence of the protecting osmolyte where urea is already there in the
> system
>
> On Sat, 21 Jul 2018, 2:21 am Mark Abraham, 
> wrote:
>
> > Hi,
> >
> > You haven't answered the question clearly. Do you care about observing
> the
> > transition (whose properties will depend on how you introduce the
> mixing),
> > or just the difference between before and after? Your proposed method is
> > ill formed because you can't continue a simulation after fundamentally
> > changing its composition. If you were watching a circus juggler keeping
> > five balls in the air, froze time and added two knives to the items in
> the
> > air, it's not going to be consistent with any pattern in which a set of
> > five balls and two knives can be juggled.
> >
> > Mark
> >
> >
> > On Fri, Jul 20, 2018, 16:12 Soham Sarkar  wrote:
> >
> > > Dear Mark,
> > > Sorry for late reply of your queries. Frankly speaking I am planning to
> > run
> > > a REMD for 50ns with protein urea and water in it, then after 50ns I
> want
> > > to add a protecting osmolyte into the system and want to continue it
> for
> > > another 50ns REMD so that I can have the effect of the protecting
> > osmolyte
> > > before and after adding it into the system. My question is, what I have
> > > planned is at all possible? How do I continue the simulation of 50ns
> for
> > > another 50ns with a protecting osmolyte in it. Is there any references
> or
> > > commnad lines or protocols to execute this type of simulation which is
> > > exclusively dedicated to the effect of a chemicals in the system.
> > > Thanks in advance.
> > > - Soham
> > >
> > > On Tue, 10 Jul 2018, 7:42 pm Soham Sarkar, 
> wrote:
> > >
> > > > Dear all,
> > > >  I am planning to do a simulation where after 50ns of simulation I
> want
> > > to
> > > > add some other chemicals in the system and continue it for another
> > 50ns,
> > > so
> > > > that I can have the effect of that chemicals exclusively before and
> > after
> > > > adding it to the system.Is it at all possible? If yes please tell me
> > the
> > > > protocol/ commands or give me some references where this type of
> > > simulation
> > > > is used. Thanks in advance.
> > > > -Soham
> > > >
> > > --
> > > 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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> > >
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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.
> > >
> > --
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Re: [gmx-users] Varying exchange probabilities between replicas in REMD

[Mark Abraham]

Hi,

It won't be constant. There's quite some literature on the topic. In
general you can't predict the probability, nor how the replicas are best
placed.

Mark

On Sat, Jul 21, 2018, 15:11 Shubhangi Gupta 
wrote:

> Hello all,
>
> I am trying to do REMD simulation following the methodology
> given by Mark Abraham (
>
> http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B
> ).
> My system is a small 34 residue protein in explicit water. I have generated
> temperatures using the server *http://folding.bmc.uu.se/remd/
> *, keeping the exchange probability
> constant at 0.2. The smallest temperature is 280K and highest temperature
> is 380K. I obtained a total of 20 replicas. However, the log file shows
> replica exchange statistics with average exchange probabilities varying
> from 0.03 to 0.28. The smaller values are for exchanges between higher
> temperature replicas.
>
> I have also tried to reproduce simulations from an old paper which has used
> AMBER software, using the temperatures mentioned there. It is for a 35
> residue protein in implicit water. The exchange probabilities vary from
> 0.32 to 0.72 when I am trying this in GROMACS.
>
> As I understand the exchange probabilities should be nearly constant. Can
> someone please help me with this. Any help is appreciated.
>
>
> Regards,
> Shubhangi Gupta
> PhD Research Scholar (YUS lab)
> Dept of Chemistry
> Indian Institute of Technology Bombay
> Powai, Mumbai-400076.
>
> e-mail ID: ignahbuhs.gup...@gmail.com
>shubhangi_gu...@iitb.ac.in
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> posting!
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>
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Re: [gmx-users] (no subject)

[Soham Sarkar]

Dear Mark,
I cant properly get your reply.. If you could elaborate it, it would be nice
- Soham

On Sat, 21 Jul 2018, 8:47 pm Mark Abraham,  wrote:

> Hi,
>
> Then all you need is the starting point for potential helix formation. You
> don't need to see it unravel.
>
> Mark
>
> On Sat, Jul 21, 2018, 05:11 Soham Sarkar  wrote:
>
> > I want to see the helix transition.. whether it is coming back or not in
> > the presence of the protecting osmolyte where urea is already there in
> the
> > system
> >
> > On Sat, 21 Jul 2018, 2:21 am Mark Abraham, 
> > wrote:
> >
> > > Hi,
> > >
> > > You haven't answered the question clearly. Do you care about observing
> > the
> > > transition (whose properties will depend on how you introduce the
> > mixing),
> > > or just the difference between before and after? Your proposed method
> is
> > > ill formed because you can't continue a simulation after fundamentally
> > > changing its composition. If you were watching a circus juggler keeping
> > > five balls in the air, froze time and added two knives to the items in
> > the
> > > air, it's not going to be consistent with any pattern in which a set of
> > > five balls and two knives can be juggled.
> > >
> > > Mark
> > >
> > >
> > > On Fri, Jul 20, 2018, 16:12 Soham Sarkar  wrote:
> > >
> > > > Dear Mark,
> > > > Sorry for late reply of your queries. Frankly speaking I am planning
> to
> > > run
> > > > a REMD for 50ns with protein urea and water in it, then after 50ns I
> > want
> > > > to add a protecting osmolyte into the system and want to continue it
> > for
> > > > another 50ns REMD so that I can have the effect of the protecting
> > > osmolyte
> > > > before and after adding it into the system. My question is, what I
> have
> > > > planned is at all possible? How do I continue the simulation of 50ns
> > for
> > > > another 50ns with a protecting osmolyte in it. Is there any
> references
> > or
> > > > commnad lines or protocols to execute this type of simulation which
> is
> > > > exclusively dedicated to the effect of a chemicals in the system.
> > > > Thanks in advance.
> > > > - Soham
> > > >
> > > > On Tue, 10 Jul 2018, 7:42 pm Soham Sarkar, 
> > wrote:
> > > >
> > > > > Dear all,
> > > > >  I am planning to do a simulation where after 50ns of simulation I
> > want
> > > > to
> > > > > add some other chemicals in the system and continue it for another
> > > 50ns,
> > > > so
> > > > > that I can have the effect of that chemicals exclusively before and
> > > after
> > > > > adding it to the system.Is it at all possible? If yes please tell
> me
> > > the
> > > > > protocol/ commands or give me some references where this type of
> > > > simulation
> > > > > is used. Thanks in advance.
> > > > > -Soham
> > > > >
> > > > --
> > > > 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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> > > >
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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.
> > > >
> > > --
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Re: [gmx-users] (no subject)

[Mark Abraham]

Hi,

If you want to see whether a helix forms in a given solution, start from a
random coil in that solution. Don't start from a helix in another solution.

Marm

On Sat, Jul 21, 2018, 17:41 Soham Sarkar  wrote:

> Dear Mark,
> I cant properly get your reply.. If you could elaborate it, it would be
> nice
> - Soham
>
> On Sat, 21 Jul 2018, 8:47 pm Mark Abraham, 
> wrote:
>
> > Hi,
> >
> > Then all you need is the starting point for potential helix formation.
> You
> > don't need to see it unravel.
> >
> > Mark
> >
> > On Sat, Jul 21, 2018, 05:11 Soham Sarkar  wrote:
> >
> > > I want to see the helix transition.. whether it is coming back or not
> in
> > > the presence of the protecting osmolyte where urea is already there in
> > the
> > > system
> > >
> > > On Sat, 21 Jul 2018, 2:21 am Mark Abraham, 
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > You haven't answered the question clearly. Do you care about
> observing
> > > the
> > > > transition (whose properties will depend on how you introduce the
> > > mixing),
> > > > or just the difference between before and after? Your proposed method
> > is
> > > > ill formed because you can't continue a simulation after
> fundamentally
> > > > changing its composition. If you were watching a circus juggler
> keeping
> > > > five balls in the air, froze time and added two knives to the items
> in
> > > the
> > > > air, it's not going to be consistent with any pattern in which a set
> of
> > > > five balls and two knives can be juggled.
> > > >
> > > > Mark
> > > >
> > > >
> > > > On Fri, Jul 20, 2018, 16:12 Soham Sarkar 
> wrote:
> > > >
> > > > > Dear Mark,
> > > > > Sorry for late reply of your queries. Frankly speaking I am
> planning
> > to
> > > > run
> > > > > a REMD for 50ns with protein urea and water in it, then after 50ns
> I
> > > want
> > > > > to add a protecting osmolyte into the system and want to continue
> it
> > > for
> > > > > another 50ns REMD so that I can have the effect of the protecting
> > > > osmolyte
> > > > > before and after adding it into the system. My question is, what I
> > have
> > > > > planned is at all possible? How do I continue the simulation of
> 50ns
> > > for
> > > > > another 50ns with a protecting osmolyte in it. Is there any
> > references
> > > or
> > > > > commnad lines or protocols to execute this type of simulation which
> > is
> > > > > exclusively dedicated to the effect of a chemicals in the system.
> > > > > Thanks in advance.
> > > > > - Soham
> > > > >
> > > > > On Tue, 10 Jul 2018, 7:42 pm Soham Sarkar, 
> > > wrote:
> > > > >
> > > > > > Dear all,
> > > > > >  I am planning to do a simulation where after 50ns of simulation
> I
> > > want
> > > > > to
> > > > > > add some other chemicals in the system and continue it for
> another
> > > > 50ns,
> > > > > so
> > > > > > that I can have the effect of that chemicals exclusively before
> and
> > > > after
> > > > > > adding it to the system.Is it at all possible? If yes please tell
> > me
> > > > the
> > > > > > protocol/ commands or give me some references where this type of
> > > > > simulation
> > > > > > is used. Thanks in advance.
> > > > > > -Soham
> > > > > >
> > > > > --
> > > > > 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
> > > >
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> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
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> > > >
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>
> * Please search t

Re: [gmx-users] topol file inaccessible

[Ali Ahmed]

hi
check your commands from misspelling

On Sat, Jul 21, 2018 at 10:08 AM, Raag Saluja  wrote:

> Hi!
> I'm simulating a heterodimer. The simulation goes really smoothly till the
> MD production step where I get an error saying the topol file is
> inaccessible. Can you please help?
>
> Thank you in advance and regards,
> Raag
> --
> 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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Re: [gmx-users] (no subject)

[Soham Sarkar]

Thanks a lot..

On Sat, 21 Jul 2018, 9:57 pm Mark Abraham,  wrote:

> Hi,
>
> If you want to see whether a helix forms in a given solution, start from a
> random coil in that solution. Don't start from a helix in another solution.
>
> Marm
>
> On Sat, Jul 21, 2018, 17:41 Soham Sarkar  wrote:
>
> > Dear Mark,
> > I cant properly get your reply.. If you could elaborate it, it would be
> > nice
> > - Soham
> >
> > On Sat, 21 Jul 2018, 8:47 pm Mark Abraham, 
> > wrote:
> >
> > > Hi,
> > >
> > > Then all you need is the starting point for potential helix formation.
> > You
> > > don't need to see it unravel.
> > >
> > > Mark
> > >
> > > On Sat, Jul 21, 2018, 05:11 Soham Sarkar  wrote:
> > >
> > > > I want to see the helix transition.. whether it is coming back or not
> > in
> > > > the presence of the protecting osmolyte where urea is already there
> in
> > > the
> > > > system
> > > >
> > > > On Sat, 21 Jul 2018, 2:21 am Mark Abraham,  >
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > You haven't answered the question clearly. Do you care about
> > observing
> > > > the
> > > > > transition (whose properties will depend on how you introduce the
> > > > mixing),
> > > > > or just the difference between before and after? Your proposed
> method
> > > is
> > > > > ill formed because you can't continue a simulation after
> > fundamentally
> > > > > changing its composition. If you were watching a circus juggler
> > keeping
> > > > > five balls in the air, froze time and added two knives to the items
> > in
> > > > the
> > > > > air, it's not going to be consistent with any pattern in which a
> set
> > of
> > > > > five balls and two knives can be juggled.
> > > > >
> > > > > Mark
> > > > >
> > > > >
> > > > > On Fri, Jul 20, 2018, 16:12 Soham Sarkar 
> > wrote:
> > > > >
> > > > > > Dear Mark,
> > > > > > Sorry for late reply of your queries. Frankly speaking I am
> > planning
> > > to
> > > > > run
> > > > > > a REMD for 50ns with protein urea and water in it, then after
> 50ns
> > I
> > > > want
> > > > > > to add a protecting osmolyte into the system and want to continue
> > it
> > > > for
> > > > > > another 50ns REMD so that I can have the effect of the protecting
> > > > > osmolyte
> > > > > > before and after adding it into the system. My question is, what
> I
> > > have
> > > > > > planned is at all possible? How do I continue the simulation of
> > 50ns
> > > > for
> > > > > > another 50ns with a protecting osmolyte in it. Is there any
> > > references
> > > > or
> > > > > > commnad lines or protocols to execute this type of simulation
> which
> > > is
> > > > > > exclusively dedicated to the effect of a chemicals in the system.
> > > > > > Thanks in advance.
> > > > > > - Soham
> > > > > >
> > > > > > On Tue, 10 Jul 2018, 7:42 pm Soham Sarkar, 
> > > > wrote:
> > > > > >
> > > > > > > Dear all,
> > > > > > >  I am planning to do a simulation where after 50ns of
> simulation
> > I
> > > > want
> > > > > > to
> > > > > > > add some other chemicals in the system and continue it for
> > another
> > > > > 50ns,
> > > > > > so
> > > > > > > that I can have the effect of that chemicals exclusively before
> > and
> > > > > after
> > > > > > > adding it to the system.Is it at all possible? If yes please
> tell
> > > me
> > > > > the
> > > > > > > protocol/ commands or give me some references where this type
> of
> > > > > > simulation
> > > > > > > is used. Thanks in advance.
> > > > > > > -Soham
> > > > > > >
> > > > > > --
> > > > > > 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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> > > > > >
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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.
> > > > > >
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
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> > or
> > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > >
> > > > --
> > > > Gromacs Users mailing list
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Re: [gmx-users] Time series of the number of atoms with the volume

[Mark Abraham]

Hi,

There's quite a few examples in its documentation, do look there for ideas.
You will need to decide some geometric criterion to define the volume of
the pore.

Mark

On Sat, Jul 21, 2018, 16:27 Mijiddorj B  wrote:

> Dear GMX users,
>
> I would like to make analysis of atom numbers within the certain volume
> such as pore of channel. If you have any experience, please advise me.
> How can I use gmx select for this purpose?
>
> Best regards,
> Miji
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Re: [gmx-users] (no subject)

[pbuscemi]

Have you tried the  "insert-chemicals-after-md" command ?

PB

> On Jul 11, 2018, at 4:50 AM, Mark Abraham  wrote:
> 
> Hi,
> 
> Are you trying to observe something about the transition, or merely the
> different end points?
> 
> Mark
> 
>> On Tue, Jul 10, 2018 at 4:12 PM Soham Sarkar  wrote:
>> 
>> Dear all,
>> I am planning to do a simulation where after 50ns of simulation I want to
>> add some other chemicals in the system and continue it for another 50ns, so
>> that I can have the effect of that chemicals exclusively before and after
>> adding it to the system.Is it at all possible? If yes please tell me the
>> protocol/ commands or give me some references where this type of simulation
>> is used. Thanks in advance.
>> -Soham
>> --
>> 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] topol file inaccessible

[Quyen V. Vu]

you should provide here more information than that

On Sat, Jul 21, 2018 at 11:42 PM, Ali Ahmed  wrote:

> hi
> check your commands from misspelling
>
> On Sat, Jul 21, 2018 at 10:08 AM, Raag Saluja 
> wrote:
>
> > Hi!
> > I'm simulating a heterodimer. The simulation goes really smoothly till
> the
> > MD production step where I get an error saying the topol file is
> > inaccessible. Can you please help?
> >
> > Thank you in advance and regards,
> > Raag
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] Tilt in the Bilayer

[atb files]

Thank you Justin Yogi Sent using Zoho Mail  On Tue, 17 Jul 2018 17:42:37 
+0530 Justin Lemkul  wrote  On 7/17/18 3:10 AM, atb files 
wrote: > > > > Dear experts,How can I find the tilt in the lipids of the 
Bilayer with respect to Bilayer normalAny gromacs tool which can do 
this.ThanksYogiSent using Zoho Mail > gmx bundle and gmx gangle can both do 
this. -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.thelemkullab.com 
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