[gmx-users] Cosine bending potential

[ARNAB MUKHERJEE]

Hi,

What is the function no. (funct) for the functional form of the bending
potential U_bend = k_theta*(cos theta - cos theta_0)^2 ?

Thanks and Regards,

Arnab
-- 
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] Using GROMACS with (AMD) OpenCL

[Gregory Man Kai Poon]

Hi Szilárd,


Thanks for your tips.  It turned out that between installing AMDGPU-PRO, then 
AMD APP SDK, the link to libopencl.so became broken.  Following your 
suggestions (if I interpreted them correctly), I linked against the copy 
installed by AMDGPU-PRO.  That resolved the error and I was able to complete 
the installation.  I also took the opportunity (as per your suggestion) to 
migrate to the 2016 release.  I had wanted to stay with 5.1.x because we had 
many simulations generated with 5.1.2 and 5.1.4 which we want to extend, and I 
was wary of potential issues with being 100% forward compatible.  I am testing 
one of these simulations now.  So far the program has not complained yet 
(expected I think) and is using the GPU.  If you know of any potential issues 
with extending simulations created by previous versions of GROMACS, I would be 
most interested in knowing them.


Thanks again,

Gregory


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Szilárd Páll 

Sent: Saturday, December 3, 2016 10:34:46 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Using GROMACS with (AMD) OpenCL

Hi Gregory,

First of all, I'd strongly recommend you to start with the 2016
release, 2016.1 has been out for some time. This will be more robust
and has a lot of performance improvement too especially on AMD (see
https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmanual.gromacs.org%2Fdocumentation%2F2016%2FReleaseNotes%2F=01%7C01%7Cgpoon%40gsu.edu%7C1c6c949cc26b455fee8f08d41b91eece%7C515ad73d8d5e4169895c9789dc742a70%7C0=4w9grG36HpkQGK%2F44RJhN3f9EQrhhcNBGxnXVxjL8WY%3D=0).

Regarding the link error, to be honest I can't tell what's wrong.
However, note that you do not necessarily need to link against the
SDK, I have clarified this in the last version of the docs:
https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmanual.gromacs.org%2Fdocumentation%2F2016%2Finstall-guide%2Findex.html%23opencl-gpu-acceleration=01%7C01%7Cgpoon%40gsu.edu%7C1c6c949cc26b455fee8f08d41b91eece%7C515ad73d8d5e4169895c9789dc742a70%7C0=VKwlCmqzHORZ8PvEEjcYzR0pXx9WtH45S7LpiVUNBY4%3D=0

While linking against the APPSDK libOpenCL _should_ work,  I'd
recommend that you try to link against the stock libOpenCL.so. If that
does not work feel free to share the cmake invocation and cache file
and we may be able to figure out something.

Cheers,
--
Szilárd


On Sat, Dec 3, 2016 at 4:02 PM, Gregory Man Kai Poon  wrote:
> Hi Milan and Szilárd,
>
>
> Many thanks for your comments.  So I installed Ubuntu 16.04, installed the 
> AMDGPU-PRO driver, installed the AMD APP SDK.  Then I attempted to install 
> GROMACS 5.1.4 as follows:
>
>
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON 
> -DGMX_USE_OPENCL=ON
>
>
> Then when I invoked make, things went fine for a bit, then halted with:
>
>
> [  1%] Built target fftwBuild
> make[2]: *** No rule to make target 
> '/home/popeye/AMDAPPSDK-3.0/lib/x86_64/libOpenCL.so', needed by 
> 'lib/libgromacs.so.1.4.0'.  Stop.
> CMakeFiles/Makefile2:2026: recipe for target 
> 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> Makefile:160: recipe for target 'all' failed
>
> I am not nearly good enough to make out what is going on, except to guess 
> that something may not be correct with the AMDAPPSDK-3.0 installation.  The 
> folder is there, and I checked the install log -- it didn't report any error 
> there.
>
>
> Thanks again for your continued help.
>
>
> Gregory
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  on behalf of Szilárd Páll 
> 
> Sent: Friday, December 2, 2016 11:22:29 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Using GROMACS with (AMD) OpenCL
>
> Hi,
>
> While for the pre-Polaris hardware Milan is right, for Polaris you
> *need* a AMDGPU-PRO (which only runs on newer distros/kernels).
>
> The current AMDGPU-PRO from the OpenCL point of view is, AFAIK more or
> less the same compiler/runtime as the last catalyst release (15.12).
>
> One notable caveat is that with AMDGPU-PRO power management seems to
> be overly aggressive (messed up?) -- at least for the load GROMACS
> generates. Uou can loose quite some performance unless you force the
> performance level to "high" (hint use radcard to set
> power_dpm_force_performance_level=high); this has been obsered on both
> Polaris and Fiji.
>
> See here:
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwiki.archlinux.org%2Findex.php%2FATI%23Dynamic_power_management=01%7C01%7Cgpoon%40gsu.edu%7Cee289917aa5a4b74dc5808d41acf7095%7C515ad73d8d5e4169895c9789dc742a70%7C0=H0FRzdUGcKtgWvVRkE7fawUX7PZtmrz%2FcwaJq7AaC%2Bo%3D=0
>
> Cheers,

Re: [gmx-users] Using GROMACS with (AMD) OpenCL

[Szilárd Páll]

Hi Gregory,

First of all, I'd strongly recommend you to start with the 2016
release, 2016.1 has been out for some time. This will be more robust
and has a lot of performance improvement too especially on AMD (see
http://manual.gromacs.org/documentation/2016/ReleaseNotes/).

Regarding the link error, to be honest I can't tell what's wrong.
However, note that you do not necessarily need to link against the
SDK, I have clarified this in the last version of the docs:
http://manual.gromacs.org/documentation/2016/install-guide/index.html#opencl-gpu-acceleration

While linking against the APPSDK libOpenCL _should_ work,  I'd
recommend that you try to link against the stock libOpenCL.so. If that
does not work feel free to share the cmake invocation and cache file
and we may be able to figure out something.

Cheers,
--
Szilárd


On Sat, Dec 3, 2016 at 4:02 PM, Gregory Man Kai Poon  wrote:
> Hi Milan and Szilárd,
>
>
> Many thanks for your comments.  So I installed Ubuntu 16.04, installed the 
> AMDGPU-PRO driver, installed the AMD APP SDK.  Then I attempted to install 
> GROMACS 5.1.4 as follows:
>
>
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON 
> -DGMX_USE_OPENCL=ON
>
>
> Then when I invoked make, things went fine for a bit, then halted with:
>
>
> [  1%] Built target fftwBuild
> make[2]: *** No rule to make target 
> '/home/popeye/AMDAPPSDK-3.0/lib/x86_64/libOpenCL.so', needed by 
> 'lib/libgromacs.so.1.4.0'.  Stop.
> CMakeFiles/Makefile2:2026: recipe for target 
> 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
> make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
> Makefile:160: recipe for target 'all' failed
>
> I am not nearly good enough to make out what is going on, except to guess 
> that something may not be correct with the AMDAPPSDK-3.0 installation.  The 
> folder is there, and I checked the install log -- it didn't report any error 
> there.
>
>
> Thanks again for your continued help.
>
>
> Gregory
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  on behalf of Szilárd Páll 
> 
> Sent: Friday, December 2, 2016 11:22:29 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Using GROMACS with (AMD) OpenCL
>
> Hi,
>
> While for the pre-Polaris hardware Milan is right, for Polaris you
> *need* a AMDGPU-PRO (which only runs on newer distros/kernels).
>
> The current AMDGPU-PRO from the OpenCL point of view is, AFAIK more or
> less the same compiler/runtime as the last catalyst release (15.12).
>
> One notable caveat is that with AMDGPU-PRO power management seems to
> be overly aggressive (messed up?) -- at least for the load GROMACS
> generates. Uou can loose quite some performance unless you force the
> performance level to "high" (hint use radcard to set
> power_dpm_force_performance_level=high); this has been obsered on both
> Polaris and Fiji.
>
> See here:
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwiki.archlinux.org%2Findex.php%2FATI%23Dynamic_power_management=01%7C01%7Cgpoon%40gsu.edu%7Cee289917aa5a4b74dc5808d41acf7095%7C515ad73d8d5e4169895c9789dc742a70%7C0=H0FRzdUGcKtgWvVRkE7fawUX7PZtmrz%2FcwaJq7AaC%2Bo%3D=0
>
> Cheers,
> --
> Szilárd
>
>
> On Fri, Dec 2, 2016 at 4:13 PM,   wrote:
>> Hi Gregory,
>> it is possible to use with both - Catalyst or AMDGPU, so you can choose. As 
>> there won't be (I think) any more updates for Catalyst, I'd prefer to use 
>> newer AMDGPU (PRO) choice. I don't have Polaris based card, only some 
>> 79xx/R9 280 (X) (uding Catalyst) and one Fury Nano (used Catalyst also, but 
>> now AMDGPU PRO). I made the Gromacs' compilation only with the Catalyst 
>> drivers, but with AMDGPU shouldn't be more complicated. Just install the 
>> system with AMDGPU (I don't know it "PRO part" is needed, probably yes) and 
>> try to compile (don't forget about the OpenCL switch). If there would be 
>> some missing libraries, than you have to install some -dev versions of 
>> packages. Probably Ubuntu has it's own way how to find the right package, 
>> but you can also use site at packages.debian.org (as Ubuntu is based on 
>> Debian).
>> Anyway I'm trying to have most of things directly from the distribution, 
>> cause it would automatically upgrades and fixes bugs. Outside the distro I 
>> have only Gromacs (performancd issues - compilation to exact machine - and 
>> several version installed) and AMDGPU PRO (on that node with Fury Nano, 
>> cause Debian doesn't have it in its repositories.
>> If any problem, plaase ask more with some details.
>>
>> Best,
>>
>> Milan
>>
>> On Fri, Dec 02, 2016 at 01:56:03PM +, Gregory Man Kai Poon wrote:
>>> Hello all,
>>>
>>>
>>> I would like to get some practical advice on setting up GROMACS with OpenCL 
>>> using an AMD GPU (an RX 480 is what I happen to have).  The AMD APP SDK 
>>> indicates that 

Re: [gmx-users] PMF decompostion

[Salman Zarrini]

Thanks David and Christopher for your responses.

I do not understand why vdW and Q are not meaningful contributors of PMF as
a biasing method, as I think one can loop over the trajectory of all the
biasing method either from US or Metadynamics and recompute the force
separating vdW and electrostatic and then project them on to the reaction
coordinate ... ,  after doing a little math, averaging, integration and
scripting you have the portion of each energy.

Concerning to the entropy and enthalpy portions, I am using covar and
anaeig to calculate eigenvectors over "non-water" ingredients for both
analyzing and fitting,  and then quasihamonic approximation and Schlitter's
formula for the entropy, but the problem is that, already the difference
between the entropy out of these two methods is something around "43 kcal/
mol" in each windows, if this is normal?
Both analyzing and fitting are "non-mass wighted" in my calculations.
Do you think I should get something close to the entropy of the
quasihamonic approximation Schlitter's formula if I use the method proposed
by you?

Cheers,

Salman Zarrini



On Sat, Dec 3, 2016 at 7:19 AM, David van der Spoel 
wrote:

> On 02/12/16 23:40, Christopher Neale wrote:
>
>> PMF gives free energy, which can not be decomposed into VDW and Q without
>> leaving a remainder, though I guess that doesn't affect your question.
>> Enthalpy is simply the average potential energy plus the pressure volume
>> component. So you can compute average potential energy VDW and Q components
>> at each umbrella if you want (from the .edr files with gmx energy). Be
>> aware that the statistical uncertainty on the enthalpy tends to be greater
>> than the relevant differences on achievable simulation timescales (i.e.,
>> convergence is hard), so you'll want to evaluate error explicitly.
>>
>> Agree with Chris here, that enthalpy and entropy are the
> thermodynamically meaningful components here. VDW and Q does not mean
> anything outside the force field definition since they can not be measured
> in any way. For more info on decomposing into enthalpy and entropy, see
> this paper: http://pubs.acs.org/doi/abs/10.1021/ct400404q
>
> 
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Salman
>> Zarrini 
>> Sent: 02 December 2016 17:16:15
>> To: gmx-us...@gromacs.org
>> Subject: [gmx-users] PMF decompostion
>>
>> Dear gromacs user,
>>
>> I was wondering if something has been already implemented in gromacs to
>> make possible the potential of mean force (PMF) decomposition into the van
>> der waals and electrostatic energies?
>>
>> Would you please also let me know if the desolvation energy originated
>> from
>> protein-water or in my case solid surface-water interaction, will be taken
>> into account automatically when one calculates the PMF in aqueous solution
>> in gromacs?
>>
>> Thanks.
>>
>> Cheers,
>> Salman Zarrini
>> --
>> 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.
>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
>
> --
> 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] Using GROMACS with (AMD) OpenCL

[Gregory Man Kai Poon]

Hi Milan and Szilárd,


Many thanks for your comments.  So I installed Ubuntu 16.04, installed the 
AMDGPU-PRO driver, installed the AMD APP SDK.  Then I attempted to install 
GROMACS 5.1.4 as follows:


cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON 
-DGMX_USE_OPENCL=ON


Then when I invoked make, things went fine for a bit, then halted with:


[  1%] Built target fftwBuild
make[2]: *** No rule to make target 
'/home/popeye/AMDAPPSDK-3.0/lib/x86_64/libOpenCL.so', needed by 
'lib/libgromacs.so.1.4.0'.  Stop.
CMakeFiles/Makefile2:2026: recipe for target 
'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
Makefile:160: recipe for target 'all' failed

I am not nearly good enough to make out what is going on, except to guess that 
something may not be correct with the AMDAPPSDK-3.0 installation.  The folder 
is there, and I checked the install log -- it didn't report any error there.


Thanks again for your continued help.


Gregory


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Szilárd Páll 

Sent: Friday, December 2, 2016 11:22:29 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Using GROMACS with (AMD) OpenCL

Hi,

While for the pre-Polaris hardware Milan is right, for Polaris you
*need* a AMDGPU-PRO (which only runs on newer distros/kernels).

The current AMDGPU-PRO from the OpenCL point of view is, AFAIK more or
less the same compiler/runtime as the last catalyst release (15.12).

One notable caveat is that with AMDGPU-PRO power management seems to
be overly aggressive (messed up?) -- at least for the load GROMACS
generates. Uou can loose quite some performance unless you force the
performance level to "high" (hint use radcard to set
power_dpm_force_performance_level=high); this has been obsered on both
Polaris and Fiji.

See here:
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwiki.archlinux.org%2Findex.php%2FATI%23Dynamic_power_management=01%7C01%7Cgpoon%40gsu.edu%7Cee289917aa5a4b74dc5808d41acf7095%7C515ad73d8d5e4169895c9789dc742a70%7C0=H0FRzdUGcKtgWvVRkE7fawUX7PZtmrz%2FcwaJq7AaC%2Bo%3D=0

Cheers,
--
Szilárd


On Fri, Dec 2, 2016 at 4:13 PM,   wrote:
> Hi Gregory,
> it is possible to use with both - Catalyst or AMDGPU, so you can choose. As 
> there won't be (I think) any more updates for Catalyst, I'd prefer to use 
> newer AMDGPU (PRO) choice. I don't have Polaris based card, only some 79xx/R9 
> 280 (X) (uding Catalyst) and one Fury Nano (used Catalyst also, but now 
> AMDGPU PRO). I made the Gromacs' compilation only with the Catalyst drivers, 
> but with AMDGPU shouldn't be more complicated. Just install the system with 
> AMDGPU (I don't know it "PRO part" is needed, probably yes) and try to 
> compile (don't forget about the OpenCL switch). If there would be some 
> missing libraries, than you have to install some -dev versions of packages. 
> Probably Ubuntu has it's own way how to find the right package, but you can 
> also use site at packages.debian.org (as Ubuntu is based on Debian).
> Anyway I'm trying to have most of things directly from the distribution, 
> cause it would automatically upgrades and fixes bugs. Outside the distro I 
> have only Gromacs (performancd issues - compilation to exact machine - and 
> several version installed) and AMDGPU PRO (on that node with Fury Nano, cause 
> Debian doesn't have it in its repositories.
> If any problem, plaase ask more with some details.
>
> Best,
>
> Milan
>
> On Fri, Dec 02, 2016 at 01:56:03PM +, Gregory Man Kai Poon wrote:
>> Hello all,
>>
>>
>> I would like to get some practical advice on setting up GROMACS with OpenCL 
>> using an AMD GPU (an RX 480 is what I happen to have).  The AMD APP SDK 
>> indicates that it supports the Catalyst Omega 15.7 driver -- is that 
>> compatible to the proprietary Catalyst driver for Linux?  Since this 
>> proprietary driver is only compatible with Ubuntu up to version 15.10, does 
>> that mean that best software configuration (say for GROMACS 5.1.4) is:
>>
>>
>> Ubuntu 15.10 + propriety Catalyst driver + AMD APP SDK
>>
>>
>> There is also a newer AMDGPU driver that works with Ubuntu 16.04 -- is that 
>> compatible with the AMD APP SDK and would allow GROMACS to be set up on a 
>> newer OS?  If I really should be going about some other way (given the GPU), 
>> please suggest also.
>>
>>
>> I have googled the subject a bit but was unable to find enough info to 
>> proceed.  Thanks in advance for your insight.
>>
>>
>> Best regards,
>>
>> Gregory
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at 
>> 

[gmx-users] Ligand-protein free binding energy is become positive

[masoud aliyar]

I’m using MM-PBSA on gromacs to calculate free binding energy of some
ligands into K-Ras (pdb-ID: 4epy). To validate MD simulation protocol and
to setup a rational threshold for evaluating the results, the co-crystal
ligand was considered as the reference ligand. Results showed that free
binding energy of reference ligand and my selected ligands have positive
quantities. Due to the fact that we are sure about the binding of reference
ligand into the binding pocket. How can we describe positive value of the
free binding energy? Results of MM-PBSA calculation for reference ligand is
as below:

Reference ligand:

van der Waal energy  =-166.208   +/-   32.482 kJ/mol

 Electrostattic energy= 144.473   +/-   15.430 kJ/mol

 Polar solvation energy   = 529.921   +/-   91.034 kJ/mol

 SASA energy  = -18.937   +/-3.458 kJ/mol

 SAV energy   =   0.000   +/-0.000 kJ/mol

 WCA energy   =   0.000   +/-0.000 kJ/mol

 Binding energy   = 489.143   +/-   46.438 kJ/mol
-- 
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] adding lcudart C++ flag + -cudart=shared NVCC flag to compile option

[Rizki Bayu]

Hello,

how can i add those two flags to their respective compiler? i want to force
Gromacs to compile using those options but im not quite used to messing
with various CMake option.

Thank you
-- 
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.