Re: [gmx-users] seeming paradox with gmx wham

[Alex]

Just to add to my question... The pull code for the umbrella sampling from each 
of the N configs, as used in Justin's tutorial, is

pull_coord1_type= umbrella
pull_coord1_geometry= distance
...
pull_coord1_dim = N N Y

So, in each of the generated pullf and pullx files we sample a flat slice at a 
given Z, and the reported forces and displacements are along Z. What appears to 
be the reaction coordinate in our case is the radius from the pore mouth, and 
one has to sample a set of hemispheres from a series of radius values. Is this 
at all a possibility?

Alex


On 3/11/2018 5:37 PM, Alex wrote:

Hi all,

I am looking at what appears to be a paradox. Consider the following 
situation: we have a graphene membrane with a single pore of a 
particular type. The pore is located at (x0, y0, h/2), where h is the 
box height. The membrane is position-restrained along its perimeter 
and immersed in a solution of NaCl. The pore is designed to trap 
anions -- and it does, if you artificially bring an anion close enough 
to the mouth of the pore and run the simulation at, say, room temp.


However, the ions do not bind by themselves. 100s of nanoseconds of 
simulations with high salt concentrations -- nothing. So, I expect a 
high barrier associated with ion dehydration when entering the pore. 
Following Justin's tutorial and generating a total of 30 1A-spaced 
configs (15 below h/2, 15 above h/2) along (x0,y0), gmx wham yields a 
6.5 kJ/mol barrier, which isn't high at all! Just from the pullf data 
when generating the configs (pull along Z with x and y restrained), 
the naive integral of the pulling force prior to overcoming the 
hydration barrier yields 4 kJ/mol -- consistent with the WHAM result. 
But in reality, ions (which aren't restrained around (x0,y0) are not 
observed to bind, which brings us to my question...


It looks like when an ion approaches the pore parallel to the membrane 
normal, the barrier is indeed low, while approach at an angle yields 
higher barriers. It appears that WHAM produces the free energy curve 
resulting from frequent sampling approach directions that have the 
lowest possible barrier. Is it possible to modify this calculation to 
give equal weight to all approach directions?


Thank you,

Alex




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[gmx-users] seeming paradox with gmx wham

[Alex]

Hi all,

I am looking at what appears to be a paradox. Consider the following 
situation: we have a graphene membrane with a single pore of a 
particular type. The pore is located at (x0, y0, h/2), where h is the 
box height. The membrane is position-restrained along its perimeter and 
immersed in a solution of NaCl. The pore is designed to trap anions -- 
and it does, if you artificially bring an anion close enough to the 
mouth of the pore and run the simulation at, say, room temp.


However, the ions do not bind by themselves. 100s of nanoseconds of 
simulations with high salt concentrations -- nothing. So, I expect a 
high barrier associated with ion dehydration when entering the pore. 
Following Justin's tutorial and generating a total of 30 1A-spaced 
configs (15 below h/2, 15 above h/2) along (x0,y0), gmx wham yields a 
6.5 kJ/mol barrier, which isn't high at all! Just from the pullf data 
when generating the configs (pull along Z with x and y restrained), the 
naive integral of the pulling force prior to overcoming the hydration 
barrier yields 4 kJ/mol -- consistent with the WHAM result. But in 
reality, ions (which aren't restrained around (x0,y0) are not observed 
to bind, which brings us to my question...


It looks like when an ion approaches the pore parallel to the membrane 
normal, the barrier is indeed low, while approach at an angle yields 
higher barriers. It appears that WHAM produces the free energy curve 
resulting from frequent sampling approach directions that have the 
lowest possible barrier. Is it possible to modify this calculation to 
give equal weight to all approach directions?


Thank you,

Alex


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[gmx-users] rvdw and rcoulomb

[Ahmed Mashaly]

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

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Re: [gmx-users] RESTARTING THE CALCULATION

[Mark Abraham]

Hi,

Exactly as you ran the original simulation, plus pass the name of the
latest checkpoint file to -cpi. Back up your files first.

Mark

On Sun, Mar 11, 2018 at 6:18 PM Neha Gupta  wrote:

> Hi gromacs users,
>
> I wanted to do simulations fro 50 ns.
>
> But, due to lack of disk space, it abruptly stopped.
>
>
> I have md.xtc, md.cpt, md.log, md_step17960400.cpt, md_prev.cpt.
>
> How to restart the calculation and complete it successfully?
>
> Thanks,
> Neha
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[gmx-users] RESTARTING THE CALCULATION

[Neha Gupta]

Hi gromacs users,

I wanted to do simulations fro 50 ns.

But, due to lack of disk space, it abruptly stopped.


I have md.xtc, md.cpt, md.log, md_step17960400.cpt, md_prev.cpt.

How to restart the calculation and complete it successfully?

Thanks,
Neha
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[gmx-users] Help with interpreting message for fatal error

[Viveca Lindahl]

Hi,

I'm running a simulation of a periodic DNA molecule. After some time I get,
sometimes the following error message:

---

A list of missing interactions:
 Proper Dih. of   3917 missing  1

Molecule type 'DNA_chain_A'
the first 10 missing interactions, except for exclusions:
 Proper Dih. atoms  414  417  418  421 global   414   417   418
421

---
Program: gmx mdrun, version 2018.1-dev-20180306-33093601f
Source file: src/gromacs/domdec/domdec_topology.cpp (line 436)
MPI rank:0 (out of 32)

Fatal error:
1 of the 10381 bonded interactions could not be calculated because some
atoms
involved moved further apart than the multi-body cut-off distance (0.5465
nm)
or the two-body cut-off distance (1.093 nm), see option -rdd, for pairs and
tabulated bonds also see option -ddcheck

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
Rank 0 [Sun Mar 11 13:37:32 2018] [c0-0c1s3n0] application called
MPI_Abort(MPI_COMM_WORLD, 1) - process 0
_pmiu_daemon(SIGCHLD): [NID 00076] [c0-0c1s3n0] [Sun Mar 11 13:37:32 2018]
PE RANK 0 exit signal Aborted
[NID 00076] 2018-03-11 13:37:32 Apid 12709959: initiated application
termination
Application 12709959 exit codes: 134
Application 12709959 resources: utime ~1083s, stime ~16s, Rss ~21376,
inblocks ~34261, outblocks ~55016
---> Reached end of run script.


How should I... proceed here? Is my system set up poorly, is it a bug in
mdrun? Suggestions appreciated.

--
Viveca
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[gmx-users] Cavity analysis of Protein

[Bhupendra Dandekar]

Dear People,

I want to study and characterize cavity of a protein. I mean i want to
characterize opening and closing of protein cavity.

Is there any tool of gromacs which will help me do that?. Are there other
softwares to do that?


Thanks
Bhupendra
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