Re: [gmx-users] Percentage of potential SASA of ligands in Gromacs??

[Dallas Warren]

SASA(exposed component) = SASA(system) - SASA(system minus component) +
SASA(component)

See https://twitter.com/dr_dbw/status/1121554245688250369 for a diagram.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Thu, 25 Apr 2019 at 04:42, Vikram Dalal 
wrote:

> Dear All,
>
>
> How to determine the SASA of different ligands in absolute values and
> percentage of their potential SASA in solution to estimate how buried they
> are in GROMACS.
> Thank you in advance.
>
>
>
>
>
>
>
> Thanks & Regards,
>
>
>
>
>
>
>
>
>
> [image: Mailtrack]
> <
> https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;
> >
> Sender
> notified by
> Mailtrack
> <
> https://mailtrack.io?utm_source=gmail_medium=signature_campaign=signaturevirality5;
> >
> 04/25/19,
> 12:12:09 AM
> --
> 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

* 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.

[gmx-users] GMX CURRENT

[Tuanan Lourenço]

Hi everyone,

I am using gmx current in 2018.2 version to get the static conductivity
through the Einstein Helfand fitting, however, I am not understanding the
output.

In the output there are some informations such as the value of
the Prefactor fit E-H: 1 / 6.0*V*k_B*T, that following the equation I think
is the factor applied to the fitting value to get the static conductivity
and also a SIGMA value.

My question is: This SIGMA value is my static conductivity? If yes, what
are the units? Because in the dsp.xvg file the unity in the y axis in the
MSD is <|M\sJ\N(t)-M\sJ\N(0)|\S2\N > / 6.0*V*k\sB\N*T / Sm^-1ps^-1. So the
SIGMA value should be S/m???

If I try do the fitting by myself and multiple the value obtained by the
Prefacactor E-H the value for the SIGMA is quite different from the gmx
current message.

Thank you very much.


Cheers

Tuanan Lourenço,



-- 
__
MSc. Tuanan C Lourenço
Ph.D Student Physical Chemistry - Universidade Federal Fluminense
Molecular Modelling and Computer Simullation Group - UFF
MOLMOD-CS WEBSITE 
-- 
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.

[gmx-users] PCA analysis and comparing extreme1 pdbs of two different simulations

[Prasanth G, Research Scholar]

Dear all,

I am interested in carrying out PCA analysis on two trajectories- 1)
protein in water and 2) protein with ligand in water.
I would like to know, if there is a procedure by which we can compare the
extreme1 pdbs (constituted by the movements that contribute to EV1) from
both the trajectories.
If yes, do we need to concatenate both the trajectories? I would be
grateful if you could share some of your ideas on this matter.

Thank you. Regards.


-- 
Regards,
Prasanth.
-- 
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.

[gmx-users] gmx select

[Pandya, Akash]

Hi all,

I'm trying to work out how many molecules of ligand and water I have within a 
certain distance. I used the gmx select command below:

gmx select -f trajectory.gro -s trajectory.tpr -oi index.dat -select 'resname 
LIG and within 0.5 of whole_res_com of resnr 1' -dt 100

However, this only outputs atomic positions. How can I get the number of "whole 
molecules"? If that makes sense? Or is there another command I can use?

Akash

-- 
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.

[gmx-users] Generation of force field for "NME " capping group

[nidhi]

Dear Gromacs users,

I want to capped the end groups of a protein chain with acetyl  (ACE) and
amine  (NME) groups. As I am using gromos96 43A1 force field and NMe is not
present in aminoacid.rtp.
In amber NME is present but not in gromos.

Anyone please suggest something how to generate force field for "Nme" in
gromos.

Regards
Nidhi
-- 
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.

[gmx-users] Best method to calculate binding free energy with GROMACS version 2016.3

[Lalehan Ozalp]

Hi everyone,
I've run several simulations with a set of 6 ligands and an enzyme (30 ns)
in water. I want to employ a method to calculate binding free energy of the
ligands but I'm aware that MMPBSA is not compatible with version 2016.3.
The forcefield I've used is charmm36-nov2018.ff.

I know I have options like PMF, BAR, FEP and LIE. However, I cannot be sure
which one to use. From the manual (or other materials) readings I've made
so far, they all seem to make sense.

Any help would be appreciated.
Thanks,

Lalehan
-- 
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.

[gmx-users] Box dimension in Umbrella Sampling

[SUSHMITA BASU]

Dear users,
I am using Gromacs 2016 to do umbrella sampling of a protein-RNA complex. I am 
following the Lemkul's tutorial of umbrella sampling, but I couldn't get how 
the box dimension was determined. I understand why for a pull of 5nm, the z 
axis of the box is set at 12 nm, but did not get how the x and y axis of the 
box is determined. This question might be very basic, but I cannot figure out 
how to do it. Kindly help me in this. Thanks in advance.
Thanks and Regards
Sushmita Basu

Thanks and regards

Sushmita Basu
Research Scholar
Department of Biotechnology
Indian Institute of Technology Kharagpur
Kharagpur 721302, India
-- 
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.

Re: [gmx-users] Failed to realloc error

[Maxim Brodmerkel]

Hi Mark,

I opened a new ticket with the number 2932 and added you in.

If you need any other files, please don’t hesitate to contact me. Thank you in 
advance!

With kind regards,
Maxim

-
Maxim Noel Brodmerkel
PhD Student, Marklund Group
Department of Chemistry - BMC,
Box 576
75123 Uppsala
Uppsala University
E-mail: maxim.brodmer...@kemi.uu.se


On 24 Apr 2019, at 16:53, Mark Abraham 
mailto:mark.j.abra...@gmail.com>> wrote:

Hi,

That sort of thing definitely should not happen for systems of size 150k
atoms. Can you please upload a .tpr and .log file to
https://redmine.gromacs.org so we can investigate?

Mark

On Wed, 24 Apr 2019 at 15:44, Maxim Brodmerkel 
mailto:maxim.brodmer...@kemi.uu.se>>
wrote:

Hello,

I encountered an error while working on simulating the satellite tobacco
necrosis virus, comprising 147960 atoms.

During the energy minimisation step using GROMACS version 2019.1 I
encountered following error:

Fatal error:
Not enough memory. Failed to realloc 18446744065119617024 bytes for
nlist->jjnr, nlist->jjnr=0x2b5cb01c9010

Or, after using 2016.6:

Fatal error:
Not enough memory. Failed to realloc -8589934592 bytes for nlist->jjnr,
nlist->jjnr=3eb9a010

I hope you could help me with fixing this error.

With kind regards,
Maxim Brodmerkel








N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r
det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r
det kan du l?sa h?r: http://www.uu.se/om-uu/dataskydd-personuppgifter/

E-mailing Uppsala University means that we will process your personal
data. For more information on how this is performed, please read here:
http://www.uu.se/en/about-uu/data-protection-policy
--
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

* 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.









När du har kontakt med oss på Uppsala universitet med e-post så innebär det att 
vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du 
läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/

E-mailing Uppsala University means that we will process your personal data. For 
more information on how this is performed, please read here: 
http://www.uu.se/en/about-uu/data-protection-policy
-- 
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.

Re: [gmx-users] clFFT error on iMAC 2017, Gromacs 2019.2, Intel Core i5, GPU Radeon Pro 555 2GB

[Szilárd Páll]

Hi,

That unfortunately looks like Apple's OpenCL not playing well with the
clFFT OpenCL library.
Avoiding offloading PME to the GPU will allow using GPU acceleration, I
think. Can you please try to run a simulation manually and pass "-pme cpu"
on the command line?

Can you also please file a report with the above content on
redmine.gromacs.org so we can follow up and address the issue in a future
release?

Cheers,
--
Szilárd


On Thu, Apr 25, 2019 at 5:48 AM Duy Tran Phuoc  wrote:

> Hi,
> Recently I compile new 2019.2 on the new iMAC with GPU Radeon Pro 555 2GB.
> Below is the compilation:
> ```
> curl http://ftp.gromacs.org/pub/gromacs/gromacs-2019.2.tar.gz --output
> gromacs-2019.2.tar.gz
> tar -xvzf gromacs-2019.2.tar.gz
> mkdir ~/gromacs
> cd ~/gromacs-2019.2
> mkdir build
> cd build
> ~/cmake/bin/cmake ../ -DGMX_MPI=ON -DGMX_GPU=ON -DGMX_CLANG_CUDA=ON
> -DGMX_USE_OPENCL=ON -DGMX_FFT_LIBRARY=fftpack -DGMX_SIMD=AVX2_256
> -DCMAKE_INSTALL_PREFIX=~/gromacs
> make -j 4
> make install
> ```
> The same situation for fftw3 compile by GROMACS.
> When I run MD with GPU, the simulation is unstable comparing to the normal
> all-on-CPU.
>
> I came back to make check to check my compilation, below is output:
>
> ```
>
> 93% tests passed, 3 tests failed out of 40
>
>
> Label Time Summary:
>
> GTest  = 156.88 sec*proc (40 tests)
>
> IntegrationTest=  60.77 sec*proc (5 tests)
>
> MpiTest=   1.92 sec*proc (3 tests)
>
> SlowTest   =  37.90 sec*proc (1 test)
>
> UnitTest   =  58.21 sec*proc (34 tests)
>
>
> Total Test time (real) = 157.81 sec
>
>
> The following tests FAILED:
>
>  29 - GmxPreprocessTests (Timeout)
>
>  37 - MdrunTests (Failed)
>
>  40 - MdrunMpiTests (Failed)
>
> Errors while running CTest
>
> make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8
>
> make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2
>
> make[1]: *** [CMakeFiles/check.dir/rule] Error 2
> ```
> All the failed tests show the error as below:
>
> ```
>
> Program: mdrun-mpi-test, version 2019.2
>
> Source file: src/gromacs/ewald/pme-gpu-3dfft-ocl.cpp (line 62)
>
> Function:void handleClfftError(clfftStatus, const char *)
>
>
> Internal error (bug):
>
> clFFT execution failure: -57
>
>
> For more information and tips for troubleshooting, please check the GROMACS
>
> website at http://www.gromacs.org/Documentation/Errors
> ```
>
> Any suggestion whether this is a bug or something else?
> Thank you a lot for consideration.
>
> Tran Phuoc Duy.
> Tokyo Institute of Technology.
> --
> 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

* 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.

Re: [gmx-users] 2019.2 build warnings

[Szilárd Páll]

Hi Alex,

On Wed, Apr 24, 2019 at 9:59 PM Alex  wrote:

> Hi Szilárd,
>
> We are using neither Ubuntu 18.04, nor glibc 2.27, but the problem is
> most certainly there.


OK.

Can you please post the content of the directories of tests that failed? It
would be useful to know the exact software configuration (reported in the
log) and the details of the errors (reported in the mdrun.out).

Thanks,
--
Szilárd



> Until the issue is solved one way or another, we
> will be staying with 2018.1, i guess.
>

> $ lsb_release -a
>
> No LSB modules are available.
>
> Distributor ID: Ubuntu
>
> Description:Ubuntu 16.04.6 LTS
>
> Release:16.04
>
> Codename:   xenial
>
> Ubuntu GLIBC 2.23-0ubuntu11
>
>
> On 4/24/2019 4:57 AM, Szilárd Páll wrote:
> > What OS are you using? There are some known issues with the Ubuntu 18.04
> +
> > glibc 2.27 which could explain the errors.
> > --
> > Szilárd
> >
> >
> >
> >
> >>
> --
> 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

* 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.