[gmx-users] virtual site, dummy massive site

[Faezeh Pousaneh]

I have 2 questions please. They seem evident, but I need to be sure to
solve my simulation problem:

1- Does being a virtual site (charge, no mass) or a normal atom, effects on
its LJ interaction energies with rest of system?

2-  Does adding a dummy massive site (no charge, only mass) to atoms of
mono-atomic system, influences on the LJ energy of whole system?

Best regards
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[gmx-users] Restarting crashed simulation

[Ali Ahmed]

Hello GROMACS users
My MD simulation was crashed then I restarted the simulation from the point
when the point was written using this command on 64 processors: mpirun -np
64  mdrun_mpi -s md.tpr -cpi stat.cpt

After few days I got nothing in the folder usch as output.gro and I got the
following
___
Command line:
  mdrun_mpi -s md.tpr -cpi stat.cpt

Warning: No checkpoint file found with -cpi option. Assuming this is a new
run.


Back Off! I just backed up md.log to ./#md.log.2#

Running on 4 nodes with total 64 cores, 64 logical cores
  Cores per node:   16
  Logical cores per node:   16
Hardware detected on host compute-2-27.local (the node of MPI rank 0):
  CPU info:
Vendor: Intel
Brand:  Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz
SIMD instructions most likely to fit this hardware: AVX_256
SIMD instructions selected at GROMACS compile time: AVX_256

  Hardware topology: Basic

Reading file md.tpr, VERSION 2016.3 (single precision)
Changing nstlist from 10 to 40, rlist from 1 to 1.003

Will use 48 particle-particle and 16 PME only ranks
This is a guess, check the performance at the end of the log file
Using 64 MPI processes
Using 1 OpenMP thread per MPI process

Non-default thread affinity set probably by the OpenMP library,
disabling internal thread affinity
WARNING: This run will generate roughly 50657 Mb of data

starting mdrun 'Molecular Dynamics'
2500 steps,  5.0 ps.

step 888000 Turning on dynamic load balancing, because the performance loss
due to load imbalance is 8.7 %.
step 930400 Turning off dynamic load balancing, because it is degrading
performance.
step 1328000 Turning on dynamic load balancing, because the performance
loss due to load imbalance is 3.4 %.
step 1328800 Turning off dynamic load balancing, because it is degrading
performance.
step 1336000 Turning on dynamic load balancing, because the performance
loss due to load imbalance is 3.4 %.
step 1338400 Turning off dynamic load balancing, because it is degrading
performance.
step 134 Will no longer try dynamic load balancing, as it degraded
performance.
Writing final coordinates.
 Average load imbalance: 13.2 %
 Part of the total run time spent waiting due to load imbalance: 7.5 %
 Average PME mesh/force load: 1.077
 Part of the total run time spent waiting due to PP/PME imbalance: 4.1 %

NOTE: 7.5 % of the available CPU time was lost due to load imbalance
  in the domain decomposition.
  You might want to use dynamic load balancing (option -dlb.)


   Core t (s)   Wall t (s)(%)
   Time: 26331875.601   411435.556 6400.0
 4d18h17:15
 (ns/day)(hour/ns)
Performance:   10.5002.286
_

Any advise or suggestion will be helpful.

Thanks in advance
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[gmx-users] (no subject)

[Faezeh Pousaneh]

Hi,

I have a simple system of non-charged diatomic molecule, (A-B).

I expect total LJ interaction energy in such system when we put LJ
parameters of atom B zero (c6 and c12=0)  should be equal with total LJ
energy of a system containing only atom A.
Am I right?

Best regards
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Re: [gmx-users] convergence of PMF

[abhisek Mondal]

Hi,

Thank you for the comments. That was really helpful.

On Fri, Nov 17, 2017 at 7:22 PM, Peter Kroon  wrote:

>
>
> On 17-11-17 14:48, Justin Lemkul wrote:
> >
> >
> > On 11/17/17 8:47 AM, Peter Kroon wrote:
> >>
> >> On 17-11-17 14:38, Justin Lemkul wrote:
> >>>
> >>> On 11/17/17 6:28 AM, abhisek Mondal wrote:
>  Hello,
> 
>  I understand the invariant trend is the key feature to look out for
>  in this
>  case.
> 
>  But, is it possible to comment on the convergence from Force-vs-Time
>  plot ?
>  I mean, if I comment that using 0.01 nm ps-1 pull rate after 500 ps of
>  pulling the force became zero and thus the biasing potential goes
>  also to
>  zero. Hence, after 5 nm of dissociation the PMF should attain
>  convergence
>  if also invariant trend-line is found near that point.
> 
>  Does this explanation make any sense from convergence of PMF's
>  perspective ?
> >>> No, because you're conducting a non-equilibrium process, which is not
> >>> going to give you a PMF.
> >>>
> >>> Your system is changing over time due to the application of a biasing
> >>> potential. It does not make sense to say that anything there converged
> >>> based on any time-dependent quantity.
> >> But shouldn't you be able to look at the force-vs-time profiles of your
> >> windows? So that you can at least say that the force per window is
> >> equilibrated?
> >
> > The OP mentioned a PMF, which is equilibrium sampling and indeed you
> > *could* look at those forces, but then in this post it is mentioned
> > that it's a non-equilibrium SMD simulation (non-zero pull rate), so
> > no, there's nothing useful to look at here.
> >
> > I would also just bypass the forces anyway, since they are extremely
> > noisy, and compute the PMF over different windows of time. That's the
> > most straightforward way to look at convergence (and what reviewers
> > *always* ask to see in papers).
> Cheers, thanks for your insight.
>
> Peter
> >
> > -Justin
> >
> >> Peter
> >>
> >>> -Justin
> >>>
> 
>  On Thu, Nov 16, 2017 at 1:15 PM, Smith, Micholas D.  >
>  wrote:
> 
> > One way to get some degree of confidence is to use the
> > bootstrapping/error
> > analysis options provided in gmx wham. But Justin is right you are
> > looking
> > for time invariance. So: use the first portion of your trajectory
> > (say
> > first 60%) and compute the PMF, then use the first 65% of your
> > trajectory
> > and see if it has changed (and by how much), then 70%, and 80% and
> > so on.
> > If you have converged (within reason), you should see that at some
> > point,
> > as you add more time to the analysis the PMF doesn't change (in any
> > statistically significant way), when that occurs you have
> > "converged".
> >
> >
> > ===
> > Micholas Dean Smith, PhD.
> > Post-doctoral Research Associate
> > University of Tennessee/Oak Ridge National Laboratory
> > Center for Molecular Biophysics
> >
> > 
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of
> > Justin
> > Lemkul 
> > Sent: Thursday, November 16, 2017 8:04 AM
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] convergence of PMF
> >
> > On 11/16/17 3:34 AM, abhisek Mondal wrote:
> >> Hi,
> >>
> >>I have derived a PMF (protein-ligand) using umbrella sampling
> > method.
> >> But how can I comment if the obtained PMF has converged well ? What
> >> are
> > the
> >> ways to check the convergence of a PMF ?
> > How would you check convergence of any quantity? You have to
> > determine
> > if the result is changing over time, and if it is invariant
> > (within the
> > context of available statistics), then the quantity is converged.
> >
> > -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 

Re: [gmx-users] convergence of PMF

[Peter Kroon]

On 17-11-17 14:48, Justin Lemkul wrote:
>
>
> On 11/17/17 8:47 AM, Peter Kroon wrote:
>>
>> On 17-11-17 14:38, Justin Lemkul wrote:
>>>
>>> On 11/17/17 6:28 AM, abhisek Mondal wrote:
 Hello,

 I understand the invariant trend is the key feature to look out for
 in this
 case.

 But, is it possible to comment on the convergence from Force-vs-Time
 plot ?
 I mean, if I comment that using 0.01 nm ps-1 pull rate after 500 ps of
 pulling the force became zero and thus the biasing potential goes
 also to
 zero. Hence, after 5 nm of dissociation the PMF should attain
 convergence
 if also invariant trend-line is found near that point.

 Does this explanation make any sense from convergence of PMF's
 perspective ?
>>> No, because you're conducting a non-equilibrium process, which is not
>>> going to give you a PMF.
>>>
>>> Your system is changing over time due to the application of a biasing
>>> potential. It does not make sense to say that anything there converged
>>> based on any time-dependent quantity.
>> But shouldn't you be able to look at the force-vs-time profiles of your
>> windows? So that you can at least say that the force per window is
>> equilibrated?
>
> The OP mentioned a PMF, which is equilibrium sampling and indeed you
> *could* look at those forces, but then in this post it is mentioned
> that it's a non-equilibrium SMD simulation (non-zero pull rate), so
> no, there's nothing useful to look at here.
>
> I would also just bypass the forces anyway, since they are extremely
> noisy, and compute the PMF over different windows of time. That's the
> most straightforward way to look at convergence (and what reviewers
> *always* ask to see in papers).
Cheers, thanks for your insight.

Peter
>
> -Justin
>
>> Peter
>>
>>> -Justin
>>>

 On Thu, Nov 16, 2017 at 1:15 PM, Smith, Micholas D. 
 wrote:

> One way to get some degree of confidence is to use the
> bootstrapping/error
> analysis options provided in gmx wham. But Justin is right you are
> looking
> for time invariance. So: use the first portion of your trajectory
> (say
> first 60%) and compute the PMF, then use the first 65% of your
> trajectory
> and see if it has changed (and by how much), then 70%, and 80% and
> so on.
> If you have converged (within reason), you should see that at some
> point,
> as you add more time to the analysis the PMF doesn't change (in any
> statistically significant way), when that occurs you have
> "converged".
>
>
> ===
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of
> Justin
> Lemkul 
> Sent: Thursday, November 16, 2017 8:04 AM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] convergence of PMF
>
> On 11/16/17 3:34 AM, abhisek Mondal wrote:
>> Hi,
>>
>>    I have derived a PMF (protein-ligand) using umbrella sampling
> method.
>> But how can I comment if the obtained PMF has converged well ? What
>> are
> the
>> ways to check the convergence of a PMF ?
> How would you check convergence of any quantity? You have to
> determine
> if the result is changing over time, and if it is invariant
> (within the
> context of available statistics), then the quantity is converged.
>
> -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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> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
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> send a mail to gmx-users-requ...@gromacs.org.
>
>

Re: [gmx-users] convergence of PMF

[Justin Lemkul]

On 11/17/17 8:47 AM, Peter Kroon wrote:


On 17-11-17 14:38, Justin Lemkul wrote:


On 11/17/17 6:28 AM, abhisek Mondal wrote:

Hello,

I understand the invariant trend is the key feature to look out for
in this
case.

But, is it possible to comment on the convergence from Force-vs-Time
plot ?
I mean, if I comment that using 0.01 nm ps-1 pull rate after 500 ps of
pulling the force became zero and thus the biasing potential goes
also to
zero. Hence, after 5 nm of dissociation the PMF should attain
convergence
if also invariant trend-line is found near that point.

Does this explanation make any sense from convergence of PMF's
perspective ?

No, because you're conducting a non-equilibrium process, which is not
going to give you a PMF.

Your system is changing over time due to the application of a biasing
potential. It does not make sense to say that anything there converged
based on any time-dependent quantity.

But shouldn't you be able to look at the force-vs-time profiles of your
windows? So that you can at least say that the force per window is
equilibrated?


The OP mentioned a PMF, which is equilibrium sampling and indeed you 
*could* look at those forces, but then in this post it is mentioned that 
it's a non-equilibrium SMD simulation (non-zero pull rate), so no, 
there's nothing useful to look at here.


I would also just bypass the forces anyway, since they are extremely 
noisy, and compute the PMF over different windows of time. That's the 
most straightforward way to look at convergence (and what reviewers 
*always* ask to see in papers).


-Justin


Peter


-Justin



On Thu, Nov 16, 2017 at 1:15 PM, Smith, Micholas D. 
wrote:


One way to get some degree of confidence is to use the
bootstrapping/error
analysis options provided in gmx wham. But Justin is right you are
looking
for time invariance. So: use the first portion of your trajectory (say
first 60%) and compute the PMF, then use the first 65% of your
trajectory
and see if it has changed (and by how much), then 70%, and 80% and
so on.
If you have converged (within reason), you should see that at some
point,
as you add more time to the analysis the PMF doesn't change (in any
statistically significant way), when that occurs you have "converged".


===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin
Lemkul 
Sent: Thursday, November 16, 2017 8:04 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] convergence of PMF

On 11/16/17 3:34 AM, abhisek Mondal wrote:

Hi,

   I have derived a PMF (protein-ligand) using umbrella sampling

method.

But how can I comment if the obtained PMF has converged well ? What
are

the

ways to check the convergence of a PMF ?

How would you check convergence of any quantity? You have to determine
if the result is changing over time, and if it is invariant (within the
context of available statistics), then the quantity is converged.

-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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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] convergence of PMF

[Peter Kroon]

On 17-11-17 14:38, Justin Lemkul wrote:
>
>
> On 11/17/17 6:28 AM, abhisek Mondal wrote:
>> Hello,
>>
>> I understand the invariant trend is the key feature to look out for
>> in this
>> case.
>>
>> But, is it possible to comment on the convergence from Force-vs-Time
>> plot ?
>> I mean, if I comment that using 0.01 nm ps-1 pull rate after 500 ps of
>> pulling the force became zero and thus the biasing potential goes
>> also to
>> zero. Hence, after 5 nm of dissociation the PMF should attain
>> convergence
>> if also invariant trend-line is found near that point.
>>
>> Does this explanation make any sense from convergence of PMF's
>> perspective ?
>
> No, because you're conducting a non-equilibrium process, which is not
> going to give you a PMF.
>
> Your system is changing over time due to the application of a biasing
> potential. It does not make sense to say that anything there converged
> based on any time-dependent quantity.
But shouldn't you be able to look at the force-vs-time profiles of your
windows? So that you can at least say that the force per window is
equilibrated?

Peter

>
> -Justin
>
>>
>>
>> On Thu, Nov 16, 2017 at 1:15 PM, Smith, Micholas D. 
>> wrote:
>>
>>> One way to get some degree of confidence is to use the
>>> bootstrapping/error
>>> analysis options provided in gmx wham. But Justin is right you are
>>> looking
>>> for time invariance. So: use the first portion of your trajectory (say
>>> first 60%) and compute the PMF, then use the first 65% of your
>>> trajectory
>>> and see if it has changed (and by how much), then 70%, and 80% and
>>> so on.
>>> If you have converged (within reason), you should see that at some
>>> point,
>>> as you add more time to the analysis the PMF doesn't change (in any
>>> statistically significant way), when that occurs you have "converged".
>>>
>>>
>>> ===
>>> Micholas Dean Smith, PhD.
>>> Post-doctoral Research Associate
>>> University of Tennessee/Oak Ridge National Laboratory
>>> Center for Molecular Biophysics
>>>
>>> 
>>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
>>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin
>>> Lemkul 
>>> Sent: Thursday, November 16, 2017 8:04 AM
>>> To: gmx-us...@gromacs.org
>>> Subject: Re: [gmx-users] convergence of PMF
>>>
>>> On 11/16/17 3:34 AM, abhisek Mondal wrote:
 Hi,

   I have derived a PMF (protein-ligand) using umbrella sampling
>>> method.
 But how can I comment if the obtained PMF has converged well ? What
 are
>>> the
 ways to check the convergence of a PMF ?
>>> How would you check convergence of any quantity? You have to determine
>>> if the result is changing over time, and if it is invariant (within the
>>> context of available statistics), then the quantity is converged.
>>>
>>> -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.
>>>
>>
>>
>


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Re: [gmx-users] convergence of PMF

[Justin Lemkul]

On 11/17/17 6:28 AM, abhisek Mondal wrote:

Hello,

I understand the invariant trend is the key feature to look out for in this
case.

But, is it possible to comment on the convergence from Force-vs-Time plot ?
I mean, if I comment that using 0.01 nm ps-1 pull rate after 500 ps of
pulling the force became zero and thus the biasing potential goes also to
zero. Hence, after 5 nm of dissociation the PMF should attain convergence
if also invariant trend-line is found near that point.

Does this explanation make any sense from convergence of PMF's perspective ?


No, because you're conducting a non-equilibrium process, which is not 
going to give you a PMF.


Your system is changing over time due to the application of a biasing 
potential. It does not make sense to say that anything there converged 
based on any time-dependent quantity.


-Justin




On Thu, Nov 16, 2017 at 1:15 PM, Smith, Micholas D. 
wrote:


One way to get some degree of confidence is to use the bootstrapping/error
analysis options provided in gmx wham. But Justin is right you are looking
for time invariance. So: use the first portion of your trajectory (say
first 60%) and compute the PMF, then use the first 65% of your trajectory
and see if it has changed (and by how much), then 70%, and 80% and so on.
If you have converged (within reason), you should see that at some point,
as you add more time to the analysis the PMF doesn't change (in any
statistically significant way), when that occurs you have "converged".


===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin
Lemkul 
Sent: Thursday, November 16, 2017 8:04 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] convergence of PMF

On 11/16/17 3:34 AM, abhisek Mondal wrote:

Hi,

  I have derived a PMF (protein-ligand) using umbrella sampling

method.

But how can I comment if the obtained PMF has converged well ? What are

the

ways to check the convergence of a PMF ?

How would you check convergence of any quantity? You have to determine
if the result is changing over time, and if it is invariant (within the
context of available statistics), then the quantity is converged.

-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
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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] Metal interactions with proteins

[Justin Lemkul]

On 11/17/17 2:30 AM, RAHUL SURESH wrote:

Dear Justin

I have tried various measures to over come it.

1. I added Cu in merged.rtp and still the error prevails.





*Error: Fatal error:in .rtp file in residue ions at line:Cu*


This appears to indicate an incorrectly formatted .rtp entry.


2. I added TER in the pdb file and still the same error. Then I removed Cu
from merged.rtp and again error prevails.


pdb2gmx can't process any residue not properly entered into the .rtp 
file, so if you removed it, naturally you're going to get an error. 
Solve problem (1) before doing anything else.


-Justin





*Error: Fatal error:Residue 'Cu' not found in residue topology database*
last few lines of my pdb




*ATOM319  OT2 ALA42   4.613   5.549   2.283  0.00
0.00   O  TER 320  ALA42 ATOM321  Cu
0   1.905  -0.009  -4.349  0.00  0.00  Cu  END*

I changed Cu atom number to 43 and also 1 but no use.
I added addition TER after 320 then again the error remains.

Please help me.


On Fri, Nov 17, 2017 at 1:42 AM, Justin Lemkul  wrote:



On 11/16/17 1:53 PM, RAHUL SURESH wrote:


Dear Justin

Why is there no aminoacids.rtp file in charmm36ff?


Because the way the CHARMM topology and parameter files are constructed
makes it nearly impossible to actually write out only certain types of
molecules, we lumped (almost) everything into one file called "merged.rtp."
The only exception is the nucleic acid files, which are separate (again, by
necessity due to how CHARMM works).

As mentioned before I have added the metal ion parameters in nonbonded.itp,

ions.ipt and atomtypes.itp. While performing simulation using the command
*"gmx
pdb2gmx -f cu.pdb -o cu.gro -p cu.top" *I receive the following error

"Residue 'Cu' not found in residue topology database"

There describe a note* "*

*Warning: Starting residue Cu43 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".*
How do i debug this?


It appears pdb2gmx is interpreting your Cu ion as part of the same chain
as a protein. Separate it using TER or a different chain identifier so that
pdb2gmx doesn't try to make it some kind of terminus.


-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] convergence of PMF

[abhisek Mondal]

Hello,

I understand the invariant trend is the key feature to look out for in this
case.

But, is it possible to comment on the convergence from Force-vs-Time plot ?
I mean, if I comment that using 0.01 nm ps-1 pull rate after 500 ps of
pulling the force became zero and thus the biasing potential goes also to
zero. Hence, after 5 nm of dissociation the PMF should attain convergence
if also invariant trend-line is found near that point.

Does this explanation make any sense from convergence of PMF's perspective ?



On Thu, Nov 16, 2017 at 1:15 PM, Smith, Micholas D. 
wrote:

> One way to get some degree of confidence is to use the bootstrapping/error
> analysis options provided in gmx wham. But Justin is right you are looking
> for time invariance. So: use the first portion of your trajectory (say
> first 60%) and compute the PMF, then use the first 65% of your trajectory
> and see if it has changed (and by how much), then 70%, and 80% and so on.
> If you have converged (within reason), you should see that at some point,
> as you add more time to the analysis the PMF doesn't change (in any
> statistically significant way), when that occurs you have "converged".
>
>
> ===
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin
> Lemkul 
> Sent: Thursday, November 16, 2017 8:04 AM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] convergence of PMF
>
> On 11/16/17 3:34 AM, abhisek Mondal wrote:
> > Hi,
> >
> >  I have derived a PMF (protein-ligand) using umbrella sampling
> method.
> > But how can I comment if the obtained PMF has converged well ? What are
> the
> > ways to check the convergence of a PMF ?
>
> How would you check convergence of any quantity? You have to determine
> if the result is changing over time, and if it is invariant (within the
> context of available statistics), then the quantity is converged.
>
> -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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-- 
Abhisek Mondal

*Senior Research Fellow*

*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*

*Kolkata 700032*

*INDIA*
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Re: [gmx-users] how to output intramolecular pair interaction parameters

[Srinivasa Ramisetti]

Yes your right. I tested it and found the matrix is indeed based on the 
order of atom types.


Thank you
Srinivasa
On 16/11/2017 20:50, Justin Lemkul wrote:



On 11/16/17 3:45 PM, Srinivasa Ramisetti wrote:
Exactly. I just wanted to know if we can get the order from the 
output information without calculating by hand as it is not always 
practical. Moreover, I am not sure if the order is preserved for each 
atom type. I will try this and let you know.


The matrix is probably just being established based on the order of 
parameters read. Do a simple test with 2 atom types, then 3, etc.


-Justin


Thank you,
Srinivasa
Sent from my iPhone

On 16 Nov 2017, at 20:26, Wes Barnett 
mailto:w.barn...@columbia.edu>> wrote:


On Thu, Nov 16, 2017 at 3:07 PM, Srinivasa Ramisetti <
s.b.ramise...@leeds.ac.uk> wrote:

This is continuation to my previous question. I used gmx dump to output
the 1-4 intramolecular interaction parameters. I could get the c6 and 
c12

values for all the list of 1-4 pair nteractions within my top file.
However, I could not understand the following lines in the output
information under the ffparams starting from functype[0] to 
functype[63]. I
do not understand how these 64 of c6,c12 values are related to 36 
atoms (8

atom types) that belong to my System. Could anyone explain me how can I
know which functype belongs to a particular atom/atom type?


You have 8 atomtypes, which means 8 sigmas and 8 epsilons . Here it 
is just

iterating through those atomtypes, combining the sigmas and epsilons
according to the combination rule in your force field, and then 
calculating

and storing c6 and c12 in memory (8x8=64). I'm not sure what order it
processes things in though. Try doing some of the combining by hand 
and see

what matches up.


--
James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group 
Columbia University
w.barn...@columbia.edu
http://wbarnett.us
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