[gmx-users] New DSSP vs do_dssp (gromacs-4.5.4)

[Ahmad Randy]

Hi All,

I understand that there were already some discussions about new DSSP exec with 
do_dssp in gromacs-4.5.4. I just want to make clear, is it true that this two 
DSSP and do_dssp do not compatible each other? 

I was running in Ubuntu 10.04, and this is what I got:

            do_dssp -f 300K.trr -s 300K.tpr -o dssp

I choose 5 'Mainchain'

            Fatal error:
            Failed to execute command: /home/madndy/dssp/dssp -na ddkbeHeQ 
ddvDjL4J > /dev/null 2> /dev/null


I already set the "export DSSP=/home/madndy/dssp/dssp", and also try the latest 
do_dssp.c (from gromacs-4.6) file for instalation. Still didn't work.

Are there are any suggestion or correction in my step? Or what version of 
gromacs that work well with DSSP? Or should I get the older version of DSSP 
that work with do_dssp? And where can I find the older version of DSSP because 
I can't find the older version in: http://swift.cmbi.ru.nl/gv/dssp/ . 

Thanx,
Randy-- 
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Re: [gmx-users] Error while running methane in water simulation

[Justin A. Lemkul]

vivek sharma wrote:

Hi there,
I am trying to run the free energy tutorial by David mobley mentioned at 
/*h**ttp://www.dillgroup.ucsf.edu/group/wiki/index.php?title=Free_Energy:_Tutorial 
*/
While running a test run for lambda value of 0, I found that there is 
some problem with the generated trajectory, I observed the distorted 
(straight lines running between box edges) methane structure in the 
water box while viewing the co-ordinate movie.
Thinking that, this scenario relates to the periodic boundary 
conditions. I checked the parameter file where *pbc = xyz.


*Please suggest what may be the reason for the distortion in methane 
during simulation.*

*


This outcome is the expected result of PBC.  You need to post-process the 
trajectory to account for this behavior.  See the workflow here:


http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin

--


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


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[gmx-users] Particle Insertion Method tpi - units and compensation of charged system

[Kathleen Kirchner]

Dear all,

I'm using gromacs particle insertion method (integrater = tpi) to obtain 
the excess chemical potential of single charged atoms.


On analyzing my results, two questions occurred to me:

1. The units for \mu_excess = -k_B T log _N are given 
according to tpi.xvg in kJ/mol*nm^3, which is kind of an energy density 
and not an energy unit. So what does it mean? Is it normalized to any 
volume? Maybe I'm missing some important point.


2. Is there a correction implemented for systems with a total net charge 
not equal to zero? I'm trying to get the solubility of CO_2 in Ionic 
Liquid, therefore I fear, the response of the system (which has zero net 
charge) on inserting particles with 0.7 e and -0.35 e will be quite huge.



Best regards
Kathleen


--
Kathleen Kirchner
PhD student
Max Planck Institute for Mathematics in the Sciences
(MPI f. Mathematik in den Naturwissenschaften)
Inselstr. 22-26, D04103 Leipzig
e-mail: kirch...@mis.mpg.de
web: http://www.mis.mpg.de/scicomp/CompPhysChem/
Tel +49 341 9959 722
Fax +49 341 9959 999

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[gmx-users] Re: Implicit solvent problems

[liaoxyi]

Dear all,

Thank you for giving me some hints for my problems.

The problems has been solved now, the key is

to adjust the gb_dielectric_offset to a smaller value like 0.05，

then theminimizationgets going normally.

Subsequently, the NVT goes well.

Still, I don’t quite understand what role

thegb_dielectric_offsetactually plays ?

 

Kiara

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Re: [gmx-users] Re: Implicit solvent problems

[Mark Abraham]

On 14/10/2011 12:38 AM, liaoxyi wrote:


Dear all,

Thank you for giving me some hints for my problems.

The problems has been solved now, the key is

to adjust the gb_dielectric_offset to a smaller value like 0.05,

then the /minimization /gets going normally.



You should use the value recommended for the model you are implementing 
- the default is suitable for the models in GROMACS.



Subsequently, the NVT goes well.

Still, I don't quite understand what role

the gb_dielectric_offset actually plays ?



You will need to read some literature here - and should have done before 
changing the default values :-). I suggest starting with the OBC paper 
referenced in the manual.


Mark
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Re: [gmx-users] New DSSP vs do_dssp (gromacs-4.5.4)

[Mark Abraham]

On 13/10/2011 8:16 PM, Ahmad Randy wrote:

Hi All,

I understand that there were already some discussions about new DSSP 
exec with do_dssp in gromacs-4.5.4. I just want to make clear, is it 
true that this two DSSP and do_dssp do not compatible each other?


If the new DSSP requires the code in do_dssp to be updated, that hasn't 
happened, and likely won't happen for a while. If someone can 
substantiate that it needs a change, and file a GROMACS Redmine issue 
describing what needs to happen, then it will be considered for the 4.6 
release.




I was running in Ubuntu 10.04, and this is what I got:

do_dssp -f 300K.trr -s 300K.tpr -o dssp

I choose 5 'Mainchain'

Fatal error:
Failed to execute command: /home/madndy/dssp/dssp -na ddkbeHeQ 
ddvDjL4J > /dev/null 2> /dev/null



I already set the "export DSSP=/home/madndy/dssp/dssp", and also try 
the latest do_dssp.c (from gromacs-4.6) file for instalation. Still 
didn't work.


Are there are any suggestion or correction in my step? Or what version 
of gromacs that work well with DSSP? Or should I get the older version 
of DSSP that work with do_dssp?


I think that is the most reliable approach.

And where can I find the older version of DSSP because I can't find 
the older version in: http://swift.cmbi.ru.nl/gv/dssp/ .


They say it is available. Please ask them.

Mark
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Re: [gmx-users] New DSSP vs do_dssp (gromacs-4.5.4)

[lina]

On Thu, Oct 13, 2011 at 5:16 PM, Ahmad Randy  wrote:

> Hi All,
>
> I understand that there were already some discussions about new DSSP exec
> with do_dssp in gromacs-4.5.4. I just want to make clear, is it true that
> this two DSSP and do_dssp do not compatible each other?
>
> I was running in Ubuntu 10.04, and this is what I got:
>
> do_dssp -f 300K.trr -s 300K.tpr -o dssp
>
> I choose 5 'Mainchain'
>
> Fatal error:
> Failed to execute command: /home/madndy/dssp/dssp -na ddkbeHeQ
> ddvDjL4J > /dev/null 2> /dev/null
>
>
> I already set the "export DSSP=/home/madndy/dssp/dssp", and also try the
> latest do_dssp.c (from gromacs-4.6) file for instalation. Still didn't work.
>
> Are there are any suggestion or correction in my step? Or what version of
> gromacs that work well with DSSP? Or should I get the older version of DSSP
> that work with do_dssp? And where can I find the older version of DSSP
> because I can't find the older version in:
> http://swift.cmbi.ru.nl/gv/dssp/ .
>

http://biskit.pasteur.fr/install/applications/dssp

You may click above link (untested, be careful).


> Thanx,
> Randy
>
> --
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[gmx-users] where are Density and Volume?

[Yao Yao]

Hi,

I wanna get Density and Volume of my system after simulation.
I found in tutorials by Justin and kerrigan?, that g_energy -f *.edr -o should 
work,
but I do not find in my version 4.5.1 and 4.5.4. That is kind of weird.

Thanks,

Yao-- 
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Re: [gmx-users] where are Density and Volume?

[Justin A. Lemkul]

Yao Yao wrote:

Hi,

I wanna get Density and Volume of my system after simulation.
I found in tutorials by Justin and kerrigan?, that g_energy -f *.edr -o 
should work,

but I do not find in my version 4.5.1 and 4.5.4. That is kind of weird.



Was it an NVT simulation?  If so, those terms are not written because they are, 
by definition, constant.


-Justin

--


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


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Re: [gmx-users] where are Density and Volume?

[Justin A. Lemkul]

Yao Yao wrote:

Hi Justin,

It is NVE. Is there a consistent way I can know my D and V?



Then you've got the same case as NVT (for these values, anyway) - volume and 
density are fixed at whatever value they started at.  editconf should have 
printed this somewhere along the way.


-Justin


Thanks,

Yao


*From:* Justin A. Lemkul 
*To:* Yao Yao ; Discussion list for GROMACS users 


*Sent:* Thursday, October 13, 2011 9:58 AM
*Subject:* Re: [gmx-users] where are Density and Volume?



Yao Yao wrote:
 > Hi,
 >
 > I wanna get Density and Volume of my system after simulation.
 > I found in tutorials by Justin and kerrigan?, that g_energy -f *.edr 
-o should work,

 > but I do not find in my version 4.5.1 and 4.5.4. That is kind of weird.
 >

Was it an NVT simulation?  If so, those terms are not written because 
they are, by definition, constant.


-Justin

-- 

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






--


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


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Re: [gmx-users] where are Density and Volume?

[Yao Yao]

Hi Justin,

thanks,

that is just initial value, no fluctuation over time.

yao  



From: Justin A. Lemkul 
To: Discussion list for GROMACS users 
Sent: Thursday, October 13, 2011 10:24 AM
Subject: Re: [gmx-users] where are Density and Volume?



Yao Yao wrote:
> Hi Justin,
> 
> It is NVE. Is there a consistent way I can know my D and V?
> 

Then you've got the same case as NVT (for these values, anyway) - volume and 
density are fixed at whatever value they started at.  editconf should have 
printed this somewhere along the way.

-Justin

> Thanks,
> 
> Yao
> 
> 
> *From:* Justin A. Lemkul 
> *To:* Yao Yao ; Discussion list for GROMACS users 
> 
> *Sent:* Thursday, October 13, 2011 9:58 AM
> *Subject:* Re: [gmx-users] where are Density and Volume?
> 
> 
> 
> Yao Yao wrote:
>  > Hi,
>  >
>  > I wanna get Density and Volume of my system after simulation.
>  > I found in tutorials by Justin and kerrigan?, that g_energy -f *.edr -o 
>should work,
>  > but I do not find in my version 4.5.1 and 4.5.4. That is kind of weird.
>  >
> 
> Was it an NVT simulation?  If so, those terms are not written because they 
> are, by definition, constant.
> 
> -Justin
> 
> -- 
> 
> 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
> 
> 
> 
> 

-- 

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


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> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> 
> 

-- 

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


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Re: [gmx-users] where are Density and Volume?

[Justin A. Lemkul]

Yao Yao wrote:

Hi Justin,

thanks,

that is just initial value, no fluctuation over time.



Right.  The volume is constant, therefore the initial values of density and 
volume are always the same.


-Justin

yao  



*From:* Justin A. Lemkul 
*To:* Discussion list for GROMACS users 
*Sent:* Thursday, October 13, 2011 10:24 AM
*Subject:* Re: [gmx-users] where are Density and Volume?



Yao Yao wrote:
 > Hi Justin,
 >
 > It is NVE. Is there a consistent way I can know my D and V?
 >

Then you've got the same case as NVT (for these values, anyway) - volume 
and density are fixed at whatever value they started at.  editconf 
should have printed this somewhere along the way.


-Justin

 > Thanks,
 >
 > Yao
 >
 > 
 > *From:* Justin A. Lemkul mailto:jalem...@vt.edu>>
 > *To:* Yao Yao mailto:ya...@ymail.com>>; Discussion 
list for GROMACS users >

 > *Sent:* Thursday, October 13, 2011 9:58 AM
 > *Subject:* Re: [gmx-users] where are Density and Volume?
 >
 >
 >
 > Yao Yao wrote:
 >  > Hi,
 >  >
 >  > I wanna get Density and Volume of my system after simulation.
 >  > I found in tutorials by Justin and kerrigan?, that g_energy -f 
*.edr -o should work,
 >  > but I do not find in my version 4.5.1 and 4.5.4. That is kind of 
weird.

 >  >
 >
 > Was it an NVT simulation?  If so, those terms are not written because 
they are, by definition, constant.

 >
 > -Justin
 >
 > -- 
 >
 > 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
 >
 > 
 >
 >

-- 

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


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Blacksburg, VA
 > jalemkul[at]vt.edu | (540) 231-9080
 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 >
 > 
 >
 >

-- 

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


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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


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Re: [gmx-users] where are Density and Volume?

[Yao Yao]

Hi, Justin

Ok, I see the problem. Like your tutorial, I used cpt for NVT/NPT to 
mdrun/continue NVE production run.
So though I did not set V or P constraint in NVE mdp, it still keeps them as 
constant, like my NVE did not work.
Am I supposed to do so if I wanna simulate NVE?

Thanks,

Yao



From: Justin A. Lemkul 
To: Discussion list for GROMACS users 
Sent: Thursday, October 13, 2011 10:42 AM
Subject: Re: [gmx-users] where are Density and Volume?



Yao Yao wrote:
> Hi Justin,
> 
> thanks,
> 
> that is just initial value, no fluctuation over time.
> 

Right.  The volume is constant, therefore the initial values of density and 
volume are always the same.

-Justin

> yao  
> 
> *From:* Justin A. Lemkul 
> *To:* Discussion list for GROMACS users 
> *Sent:* Thursday, October 13, 2011 10:24 AM
> *Subject:* Re: [gmx-users] where are Density and Volume?
> 
> 
> 
> Yao Yao wrote:
>  > Hi Justin,
>  >
>  > It is NVE. Is there a consistent way I can know my D and V?
>  >
> 
> Then you've got the same case as NVT (for these values, anyway) - volume and 
> density are fixed at whatever value they started at.  editconf should have 
> printed this somewhere along the way.
> 
> -Justin
> 
>  > Thanks,
>  >
>  > Yao
>  >
>  > 
>  > *From:* Justin A. Lemkul mailto:jalem...@vt.edu>>
>  > *To:* Yao Yao mailto:ya...@ymail.com>>; Discussion list 
>for GROMACS users mailto:gmx-users@gromacs.org>>
>  > *Sent:* Thursday, October 13, 2011 9:58 AM
>  > *Subject:* Re: [gmx-users] where are Density and Volume?
>  >
>  >
>  >
>  > Yao Yao wrote:
>  >  > Hi,
>  >  >
>  >  > I wanna get Density and Volume of my system after simulation.
>  >  > I found in tutorials by Justin and kerrigan?, that g_energy -f *.edr -o 
>should work,
>  >  > but I do not find in my version 4.5.1 and 4.5.4. That is kind of weird.
>  >  >
>  >
>  > Was it an NVT simulation?  If so, those terms are not written because they 
>are, by definition, constant.
>  >
>  > -Justin
>  >
>  > -- 
>  >
>  > 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
>  >
>  > 
>  >
>  >
> 
> -- 
> 
> 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@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-requ...@gromacs.org 
> .
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> Blacksburg, VA
>  > jalemkul[at]vt.edu | (540) 231-9080
>  > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>  >
>  > 
>  >
>  >
> 
> -- 
> 
> 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@gromacs.org 
> 
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
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> .
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> 

-- 

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


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Re: [gmx-users] where are Density and Volume?

[Justin A. Lemkul]

Yao Yao wrote:

Hi, Justin

Ok, I see the problem. Like your tutorial, I used cpt for NVT/NPT to 
mdrun/continue NVE production run.
So though I did not set V or P constraint in NVE mdp, it still keeps 
them as constant, like my NVE did not work.

Am I supposed to do so if I wanna simulate NVE?



NVE will keep the energy constant under the set conditions.  I do not know why P 
is constant; with V being constant (by definition), P should fluctuate under 
NVE.  Providing a .cpt file from a previous NVT or NPT will define the 
conditions under which NVE is run (i.e. what energy is to be maintained).


-Justin


Thanks,

Yao


*From:* Justin A. Lemkul 
*To:* Discussion list for GROMACS users 
*Sent:* Thursday, October 13, 2011 10:42 AM
*Subject:* Re: [gmx-users] where are Density and Volume?



Yao Yao wrote:
 > Hi Justin,
 >
 > thanks,
 >
 > that is just initial value, no fluctuation over time.
 >

Right.  The volume is constant, therefore the initial values of density 
and volume are always the same.


-Justin

 > yao 
 > 

 > *From:* Justin A. Lemkul mailto:jalem...@vt.edu>>
 > *To:* Discussion list for GROMACS users >

 > *Sent:* Thursday, October 13, 2011 10:24 AM
 > *Subject:* Re: [gmx-users] where are Density and Volume?
 >
 >
 >
 > Yao Yao wrote:
 >  > Hi Justin,
 >  >
 >  > It is NVE. Is there a consistent way I can know my D and V?
 >  >
 >
 > Then you've got the same case as NVT (for these values, anyway) - 
volume and density are fixed at whatever value they started at.  
editconf should have printed this somewhere along the way.

 >
 > -Justin
 >
 >  > Thanks,
 >  >
 >  > Yao
 >  >
 >  > 

 >  > *From:* Justin A. Lemkul mailto:jalem...@vt.edu> 
>>
 >  > *To:* Yao Yao mailto:ya...@ymail.com> 
>>; Discussion list for 
GROMACS users mailto:gmx-users@gromacs.org> 
>>

 >  > *Sent:* Thursday, October 13, 2011 9:58 AM
 >  > *Subject:* Re: [gmx-users] where are Density and Volume?
 >  >
 >  >
 >  >
 >  > Yao Yao wrote:
 >  >  > Hi,
 >  >  >
 >  >  > I wanna get Density and Volume of my system after simulation.
 >  >  > I found in tutorials by Justin and kerrigan?, that g_energy -f 
*.edr -o should work,
 >  >  > but I do not find in my version 4.5.1 and 4.5.4. That is kind 
of weird.

 >  >  >
 >  >
 >  > Was it an NVT simulation?  If so, those terms are not written 
because they are, by definition, constant.

 >  >
 >  > -Justin
 >  >
 >  > -- 
 >  >
 >  > 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
 >  >
 >  > 
 >  >
 >  >
 >
 > -- 
 >
 > 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 listgmx-users@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-requ...@gromacs.org 
 
>.

 > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 > Blacksburg, VA
 >  > jalemkul[at]vt.edu | (540) 231-9080
 >  > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 >  >
 >  > 
 >  >
 >  >
 >
 > -- 
 >
 > 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 listgmx-users@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

[gmx-users] pdb2gmx charmm topology lipid

[ram bio]

Dear Justin,

Thanks for the suggestions.

> The lipids are built into the CHARMM27 implementation in Gromacs.  You can
> generate their topology with pdb2gmx.  Run pdb2gmx on a single lipid,
> convert it to an .itp file, and #include it in the topology.

I separated out one lipid from the POPC bilayer (250 lipids) i am
having (attached -popc.pdb) and modified (popcatomtype.pdb) the atom
names as per the
/usr/local/gromacs/share/gromacs/top/charmm27.ff/lipids.rtp file. Then
i executed

pdb2gmx -f popcatomtype.pdb -o popcatom.gro

choosing option 8 for Charmm ff
&1 for water model

but, i am getting an error as below:

Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.r2b
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.r2b
Reading popcatomtype.pdb...
Read 52 atoms
Analyzing pdb file
Splitting PDB chains based on TER records or changing chain id.
There are 1 chains and 0 blocks of water and 0 residues with 52 atoms

  chain  #res #atoms
  1 'C' 1 52


WARNING: there were 0 atoms with zero occupancy and 52 atoms with
 occupancy unequal to one (out of 52 atoms). Check your pdb file.

Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/atomtypes.atp
Atomtype 1
Reading residue database... (charmm27)
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.rtp
Residue 41
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.rtp
Residue 45
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/lipids.rtp
Residue 57
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.rtp
Residue 61
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/lipids.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.c.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.c.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.c.tdb

Back Off! I just backed up topol.top to ./#topol.top.30#
Processing chain 1 'C' (52 atoms, 1 residues)
There are 1 donors and 0 acceptors
There are 0 hydrogen bonds
Warning: Starting residue POP0 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully

---
Program pdb2gmx, VERSION 4.5.4
Source code file: resall.c, line: 581

Fatal error:
Residue 'POP' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Please let me know your suggestions to fix this error.

Thanks,

Pramod


On Wed, Oct 12, 2011 at 8:21 PM, Justin A. Lemkul  wrote:
>
>
> ram bio wrote:
>>
>> Dear Justin,
>>
>> Thanks.
>>
>> The POPC bilayer i am using is with berger lipids, corrected for dihedrals
>> so as to be compatible with the OPLS FF for aminoacids.
>>
>
> I think significantly more parameters than just dihedrals need to be altered
> to make the Berger united-atom force field compatible with OPLS.
>
>> While searching for the literature on compatibility of lipid FF and
>> protein FF, I found few references where similar modification was done for
>> DOPC lipid bilayer  and were suitable with various FF for proteins and also
>> with CHARMM FF:
>>
>> 1. Membrane protein simulations with a united-atom lipid and all-atom
>> protein model: lipid–protein interactions, side chain transfer free energies
>> and model proteins.J. Phys.: Condens. Matter 18 (2006) S1221–S1234
>>
>> 2. Combination of the CHARMM27 Force Field with United-Atom Lipid Force
>> Fields.J Comput Chem 32: 1400–1410, 2011.
>>
>> I don't have the lipid bilayer with their  itp files with CHARMM FF
>> parameterization. Please could you inform me where to obtain them, so that i
>> can use the lipid bilayer structure for embedding the protein and use the
>> related CHARMM FF parameterised itp in the topology file in gromacs for MD
>> simulation.
>>
>
> The lipids are built into the CHARMM27 implementation in Gromacs.  Yo

[gmx-users] Re: pdb2gmx charmm topology lipid

[Justin A. Lemkul]

ram bio wrote:

Dear Justin,

Thanks for the suggestions.


The lipids are built into the CHARMM27 implementation in Gromacs.  You can
generate their topology with pdb2gmx.  Run pdb2gmx on a single lipid,
convert it to an .itp file, and #include it in the topology.


I separated out one lipid from the POPC bilayer (250 lipids) i am
having (attached -popc.pdb) and modified (popcatomtype.pdb) the atom
names as per the
/usr/local/gromacs/share/gromacs/top/charmm27.ff/lipids.rtp file. Then
i executed

pdb2gmx -f popcatomtype.pdb -o popcatom.gro

choosing option 8 for Charmm ff
&1 for water model

but, i am getting an error as below:

Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.r2b
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.r2b
Reading popcatomtype.pdb...
Read 52 atoms
Analyzing pdb file
Splitting PDB chains based on TER records or changing chain id.
There are 1 chains and 0 blocks of water and 0 residues with 52 atoms

  chain  #res #atoms
  1 'C' 1 52


WARNING: there were 0 atoms with zero occupancy and 52 atoms with
 occupancy unequal to one (out of 52 atoms). Check your pdb file.

Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/atomtypes.atp
Atomtype 1
Reading residue database... (charmm27)
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.rtp
Residue 41
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.rtp
Residue 45
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/lipids.rtp
Residue 57
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.rtp
Residue 61
Sorting it all out...
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/lipids.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.hdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.n.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.c.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.c.tdb
Opening force field file
/usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.c.tdb

Back Off! I just backed up topol.top to ./#topol.top.30#
Processing chain 1 'C' (52 atoms, 1 residues)
There are 1 donors and 0 acceptors
There are 0 hydrogen bonds
Warning: Starting residue POP0 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully

---
Program pdb2gmx, VERSION 4.5.4
Source code file: resall.c, line: 581

Fatal error:
Residue 'POP' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

Please let me know your suggestions to fix this error.



The answers to nearly every error message are listed either on the Gromacs 
website or in the list archive.  For instance, this happens to be one of the 
most common:


http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database

Check the .rtp file for the expected name.

-Justin

--


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 listgmx-users@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!
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Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] where are Density and Volume?

[Yao Yao]

Hi Justin,

Just curious. what is inside .cpt file,is there a way I can change it in 
readable format?
I also notice that every mdrun step I got a state.cpt and state_prev.cpt as 
well, any difference between the two?
And using .cpt seems a little faster (a couple of hours or so) than without 
using it for the same time length simulation, do you happen to know the reason?

Thanks,

yao




From: Justin A. Lemkul 
To: Discussion list for GROMACS users 
Sent: Thursday, October 13, 2011 11:28 AM
Subject: Re: [gmx-users] where are Density and Volume?



Yao Yao wrote:
> Hi, Justin
> 
> Ok, I see the problem. Like your tutorial, I used cpt for NVT/NPT to 
> mdrun/continue NVE production run.
> So though I did not set V or P constraint in NVE mdp, it still keeps them as 
> constant, like my NVE did not work.
> Am I supposed to do so if I wanna simulate NVE?
> 

NVE will keep the energy constant under the set conditions.  I do not know why 
P is constant; with V being constant (by definition), P should fluctuate under 
NVE.  Providing a .cpt file from a previous NVT or NPT will define the 
conditions under which NVE is run (i.e. what energy is to be maintained).

-Justin

> Thanks,
> 
> Yao
> 
> 
> *From:* Justin A. Lemkul 
> *To:* Discussion list for GROMACS users 
> *Sent:* Thursday, October 13, 2011 10:42 AM
> *Subject:* Re: [gmx-users] where are Density and Volume?
> 
> 
> 
> Yao Yao wrote:
>  > Hi Justin,
>  >
>  > thanks,
>  >
>  > that is just initial value, no fluctuation over time.
>  >
> 
> Right.  The volume is constant, therefore the initial values of density and 
> volume are always the same.
> 
> -Justin
> 
>  > yao  > 
>
>  > *From:* Justin A. Lemkul mailto:jalem...@vt.edu>>
>  > *To:* Discussion list for GROMACS users >
>  > *Sent:* Thursday, October 13, 2011 10:24 AM
>  > *Subject:* Re: [gmx-users] where are Density and Volume?
>  >
>  >
>  >
>  > Yao Yao wrote:
>  >  > Hi Justin,
>  >  >
>  >  > It is NVE. Is there a consistent way I can know my D and V?
>  >  >
>  >
>  > Then you've got the same case as NVT (for these values, anyway) - volume 
>and density are fixed at whatever value they started at.  editconf should have 
>printed this somewhere along the way.
>  >
>  > -Justin
>  >
>  >  > Thanks,
>  >  >
>  >  > Yao
>  >  >
>  >  > 
>  >  > *From:* Justin A. Lemkul mailto:jalem...@vt.edu> 
>>>
>  >  > *To:* Yao Yao mailto:ya...@ymail.com> 
>>>; Discussion list for 
>GROMACS users mailto:gmx-users@gromacs.org> 
>>>
>  >  > *Sent:* Thursday, October 13, 2011 9:58 AM
>  >  > *Subject:* Re: [gmx-users] where are Density and Volume?
>  >  >
>  >  >
>  >  >
>  >  > Yao Yao wrote:
>  >  >  > Hi,
>  >  >  >
>  >  >  > I wanna get Density and Volume of my system after simulation.
>  >  >  > I found in tutorials by Justin and kerrigan?, that g_energy -f *.edr 
>-o should work,
>  >  >  > but I do not find in my version 4.5.1 and 4.5.4. That is kind of 
>weird.
>  >  >  >
>  >  >
>  >  > Was it an NVT simulation?  If so, those terms are not written because 
>they are, by definition, constant.
>  >  >
>  >  > -Justin
>  >  >
>  >  > -- 
>  >  >
>  >  > 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
>  >  >
>  >  > 
>  >  >
>  >  >
>  >
>  > -- 
>  >
>  > 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@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-requ...@gromacs.org 
> >.
>  > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>  > Blacksburg, VA
>  >  > jalemkul[at]v

Re: [gmx-users] where are Density and Volume?

[Justin A. Lemkul]

Yao Yao wrote:

Hi Justin,

Just curious. what is inside .cpt file,is there a way I can change it in 
readable format?


gmxdump

I also notice that every mdrun step I got a state.cpt and state_prev.cpt 
as well, any difference between the two?


http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File

And using .cpt seems a little faster (a couple of hours or so) than 
without using it for the same time length simulation, do you happen to 
know the reason?


When supplying the .cpt to grompp, or to mdrun?  If you supply it to mdrun, the 
simulation picks up from the time in the .cpt file, not the .tpr file.


At this point, you should probably start a new thread about checkpoints, rather 
than add on to this one, as the issues are now unrelated.


-Justin



Thanks,

yao


*From:* Justin A. Lemkul 
*To:* Discussion list for GROMACS users 
*Sent:* Thursday, October 13, 2011 11:28 AM
*Subject:* Re: [gmx-users] where are Density and Volume?



Yao Yao wrote:
 > Hi, Justin
 >
 > Ok, I see the problem. Like your tutorial, I used cpt for NVT/NPT to 
mdrun/continue NVE production run.
 > So though I did not set V or P constraint in NVE mdp, it still keeps 
them as constant, like my NVE did not work.

 > Am I supposed to do so if I wanna simulate NVE?
 >

NVE will keep the energy constant under the set conditions.  I do not 
know why P is constant; with V being constant (by definition), P should 
fluctuate under NVE.  Providing a .cpt file from a previous NVT or NPT 
will define the conditions under which NVE is run (i.e. what energy is 
to be maintained).


-Justin

 > Thanks,
 >
 > Yao
 >
 > 
 > *From:* Justin A. Lemkul mailto:jalem...@vt.edu>>
 > *To:* Discussion list for GROMACS users >

 > *Sent:* Thursday, October 13, 2011 10:42 AM
 > *Subject:* Re: [gmx-users] where are Density and Volume?
 >
 >
 >
 > Yao Yao wrote:
 >  > Hi Justin,
 >  >
 >  > thanks,
 >  >
 >  > that is just initial value, no fluctuation over time.
 >  >
 >
 > Right.  The volume is constant, therefore the initial values of 
density and volume are always the same.

 >
 > -Justin
 >
 >  > yao  > 

 >  > *From:* Justin A. Lemkul mailto:jalem...@vt.edu> 
>>
 >  > *To:* Discussion list for GROMACS users  >>

 >  > *Sent:* Thursday, October 13, 2011 10:24 AM
 >  > *Subject:* Re: [gmx-users] where are Density and Volume?
 >  >
 >  >
 >  >
 >  > Yao Yao wrote:
 >  >  > Hi Justin,
 >  >  >
 >  >  > It is NVE. Is there a consistent way I can know my D and V?
 >  >  >
 >  >
 >  > Then you've got the same case as NVT (for these values, anyway) - 
volume and density are fixed at whatever value they started at.  
editconf should have printed this somewhere along the way.

 >  >
 >  > -Justin
 >  >
 >  >  > Thanks,
 >  >  >
 >  >  > Yao
 >  >  >
 >  >  > 

 >  >  > *From:* Justin A. Lemkul  >    >  > *To:* Yao Yao mailto:ya...@ymail.com> 
> 
  
> 
 
  >  > *Sent:* Thursday, October 13, 2011 9:58 AM
 >  >  > *Subject:* Re: [gmx-users] where are Density and Volume?
 >  >  >
 >  >  >
 >  >  >
 >  >  > Yao Yao wrote:
 >  >  >  > Hi,
 >  >  >  >
 >  >  >  > I wanna get Density and Volume of my system after simulation.
 >  >  >  > I found in tutorials by Justin and kerrigan?, that g_energy 
-f *.edr -o should work,
 >  >  >  > but I do not find in my version 4.5.1 and 4.5.4. That is 
kind of weird.

 >  >  >  >
 >  >  >
 >  >  > Was it an NVT simulation?  If so, those terms are not written 
because they are, by definition, constant.

 >  >  >
 >  >  > -Justin
 >  >  >
 >  >  > -- 
 >  >  >
 >  >  > 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] REMD and GBSA

[Ben Reynwar]

Hi gromacs list,

I'm about to start some REMD simulations using generalized Born
solvent on a protein of about 5000 atoms.  I have two questions, the
first of which is about gromacs, the second more about REMD in
general.

(1)
I'm getting some pretty ugly energy drift (300K->500K in 1 ns) for an
NVE MD test simulation using a 2 fs time step.  It goes away if I use
1 fs, however I was under the impression that 2 fs is normally OK.  I
was wondering whether that could be caused by the use of the cut-off
method which is required with the coloumb and VdW interactions when
using GBSA?  Or perhaps I'm doing something else wrong.  I'll include
the mdp file I'm using at the bottom of the email in case anyone feels
like pointing out my foolishness to me.

(2)
I've been analyzing some data from an REMD simulation by my
predecessor and see very slow replica flow rates.  They are about two
orders of magnitude smaller than the idealized rate of the exchange
attempt frequency multiplied by the acceptance fraction (exchanges are
attempted every 2 ps with a 0.4 acceptance fraction).  If I look at
the energy distribution for a given replica/temperature combination
over a time scale of around 1 ns, it is clearly shifted from the
average energy distribution for that temperature.  The timescale for
changes in this energy shift is around 10 ns.  My current theory for
the slow rate of replica flow is that the slow fluctuations in the
energy of the protein are limiting replica flow, since a replica with
lower than average energy will tend to remain at the bottom of the
temperature range, while those with higher than average energies will
tend to remain at the top.  Has anyone else observed this kind of
behavior?  Is my reasoning wrong in any obvious way?

Cheers,
Ben

; An energy drift simulation of TaHSP.

; 7.3.2 Preprocssing
; --
; defines pass to the preprocessor
define =

; 7.3.3 Run Control
; -
; group(s) for center of mass motion removal
comm_grps = System
; Use the MD integrator (as opposed to minimization).
integrator = md
; maximum number of steps to integrate
nsteps = 1
; remove center of mass translation and rotation around centre of mass
comm_mode = Angular
; [ps] time step for integration
dt = 0.002
; [steps] frequency of mass motion removal
nstcomm = 10
; [ps] starting time for run
tinit = 0

; 7.3.8 Output Control
; 
; [steps] freq to write velocities to trajectory
nstvout = 0
; [steps] freq to write energies to log file
nstlog = 100
; Write to energy file frequently.
nstenergy = 100
; group(s) to write to xtc trajectory
xtc_grps = System
; [real] precision to write xtc trajectory
xtc_precision = 1000
; [steps] freq to write coordinates to xtc trajectory
nstxtcout = 1000
; [steps] freq to write coordinates to trajectory
nstxout = 0
; group(s) to write to energy file
energygrps = System
; [steps] freq to write forces to trajectory
nstfout = 0

; 7.3.9 Neighbour Searching
; -
; [nm] cut-off distance for the short-range neighbor list
; For Generalized Born this must be equal to the cut-off length for
; the born radius calculation.
rlist = 1.6
; method of updating neighbor list
ns_type = grid
; [steps] freq to update neighbor list
nstlist = 1
; no periodic boundary conditions
pbc = no

; 7.3.10 Electrostatics
; -
; apply a cut-off to electostatic
coulombtype = cut-off
; coloumb cutoff radius
rcoulomb = 1.6

; 7.3.11 VdW
; --
; Dispersion correction makes no sense without box size.
DispCorr = no
; twin-range cut-off with rlist where rvdw >rlist
vdwtype = cut-off
; Increasing VdW cutoff to same as everything else.
rvdw = 1.6

; 7.3.13 Ewald
; 
; [nm] grid spacing for FFT grid when using PME
fourierspacing = 0.12
; relative strength of Ewald-shifted potential at rcoulomb
ewald_rtol = 1e-05
; interpolation order for PME, 4 cubic
pme_order = 4

; 7.3.14 Temperature Coupling
; ---
; Temperature.
ref_t = 300
; temperature coupling frequency
nsttcouple = 1
; Doing NVE simulation so no thermostat.
tcoupl = no
; couple everything to same bath
tc_grps = System
; [ps] time constant for coupling
tau_t = 0.1

; 7.3.15 Pressure Coupling
; 
; [bar] reference pressure for coupling
ref_p = 1.0
; pressure coupling in x-y-z directions
pcoupltype = isotropic
; [ps] time constant for coupling
tau_p = 2.0
; no pressure coupling if using generalized born
pcoupl = no
; [bar^-1] compressibility
compressibility = 4.5e-05

; 7.3.17 Velocity Generation
; --
; velocity generation turned off
gen_vel = no

; 7.3.18 Bonds
; 
; apply constraints to the start configuration
continuation = yes
; [degrees] maximum angle that a bond can rotate before LINCS will complain
lincs_warnangle = 30
; highest order in the expansion of the contraint coupling matrix
lincs_order = 4
; number of iterations to correct for rotational lengthening
lincs_iter = 1
; LINear 

[gmx-users] why the pressure fluctuated wildly during the simulation?

[杜波]

when i simulate in the NPT , and the parameter are set as follow,

Pcoupl   = Parrinello-Rahman
pcoupltype   = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p= 5
compressibility  = 6.5e-5
ref_p= 1.0

and the result:
Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Total Energy30582.98.1301.475  34.36  (kJ/mol)
Temperature 5002.9e-0510.6006 -3.11052e-05  (K)
Pressure1.68994  0.0441199.11 -0.0909901  (bar)

we can see the RMSD  of Pressure is so big !!!
why the pressure fluctuated wildly during the simulation?
thanks!!

regards,
Bo Du
Department of Polymer Science and Engineering,
School of Chemical Engineering and technology,
Tianjin University, Weijin Road 92, Nankai District 300072,
Tianjin City P. R. China
Tel/Fax: +86-22-27404303
E-mail: 2008d...@gmail.com
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Re: [gmx-users] why the pressure fluctuated wildly during the simulation?

[Justin A. Lemkul]

杜波 wrote:

when i simulate in the NPT , and the parameter are set as follow,

Pcoupl   = Parrinello-Rahman
pcoupltype   = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p= 5
compressibility  = 6.5e-5
ref_p= 1.0

and the result:
Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Total Energy30582.98.1301.475  34.36  (kJ/mol)
Temperature 5002.9e-0510.6006 -3.11052e-05  (K)
Pressure1.68994  0.0441199.11 -0.0909901  (bar)

we can see the RMSD  of Pressure is so big !!!
why the pressure fluctuated wildly during the simulation?


Sounds normal.

http://www.gromacs.org/Documentation/Terminology/Pressure

-Justin

--


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


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