Re: [gmx-users] Performance on multiple GPUs per node

[Szilárd Páll]

Hi,

Without details of your benchmarks it's hard to comment on why do you not
see performance improvement with multiple GPUs per node. Sharing some logs
would be helpful.

Are you comparing performance with N cores and varying number of GPUs? The
balance of hardware resources is a key factor to scaling and my guess is
that your runs are essentially CPU-bound, hence adding more GPUs does not
help.

Have a look at these papers:
https://doi.org/10.1002/jcc.24030
https://doi.org/10.1007/978-3-319-15976-8_1
especially the former covers the topic quite well and both show scaling of
<100k protein system to 32-64 nodes (dual socket/dual GPU).

Cheers,

--
Szilárd

On Fri, Dec 11, 2015 at 11:54 AM, Jens Krüger <
krue...@informatik.uni-tuebingen.de> wrote:

> Dear all,
>
> we are currently planning a new cluster at our universities compute
> centre. The big question on our side is, how many and which GPUs we should
> put into the nodes.
>
> We have access to a test system with four Tesla K80s per Node. Using one
> GPU node we can reach something like 23 ns/day for the ADH system (PME,
> cubic) which is pretty much in line with e.g.,
> http://exxactcorp.com/index.php/solution/solu_list/84
>
> When trying to use 2 or more GPUs on one node, the performance plunges to
> below 10 ns/day no matter how we split the MPI/OMP threads. Has anybody of
> you guys access to a comparable hardware setup? We would be interested in
> benchmark data answering the question: Does GROMACS-5.1 scales on more than
> one GPU per node?
>
> Thanks and best wishes,
>
> Jens
>
>
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Re: [gmx-users] using OH ions in combination with CHARMM27 force field

[soumadwip ghosh]

Thanks Justin for your help. I will carry out the simulation with 0.1M NaOH
which I had previously (the coordinate and the topology) and let you know
if the desired interactions are taking place or not.

Cheers,
Soumadwip
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[gmx-users] Performance on multiple GPUs per node

[Jens Krüger]

Dear all,

we are currently planning a new cluster at our universities compute 
centre. The big question on our side is, how many and which GPUs we 
should put into the nodes.


We have access to a test system with four Tesla K80s per Node. Using one 
GPU node we can reach something like 23 ns/day for the ADH system (PME, 
cubic) which is pretty much in line with e.g., 
http://exxactcorp.com/index.php/solution/solu_list/84


When trying to use 2 or more GPUs on one node, the performance plunges 
to below 10 ns/day no matter how we split the MPI/OMP threads. Has 
anybody of you guys access to a comparable hardware setup? We would be 
interested in benchmark data answering the question: Does GROMACS-5.1 
scales on more than one GPU per node?


Thanks and best wishes,

Jens


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[gmx-users] Regarding generating itp file.

[Raju Lunkad]

Dear GROMACS Admins,

I want to generate itp file of crystal structure ( calcium oxalate
monohyrate). Can anyone  suggest me how to generate itp file.

Thanking you,

Yours sincerely,

Raju Lunkad
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Re: [gmx-users] G53A6, non-symmetric selection metrix

[Piggot T.]

Hi Mohsen,

This table can indeed be quite confusing at first. I suggest you take a look at 
http://redmine.gromacs.org/issues/773#note-10 where there is a discussion of 
how to interpret table 8 (for a specific example, but it should highlight how 
it works). Hopefully that should answer your questions.

Cheers

Tom

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Mohsen 
Ramezanpour [ramezanpour.moh...@gmail.com]
Sent: 10 December 2015 23:42
To: Discussion list for GROMACS users
Subject: [gmx-users] G53A6, non-symmetric selection metrix

Dear All,

Reading the parameters for Gromos 53A6 ff ( article by Oostenbrink  *et al.
Journal of computational chemistry* 25.13 (2004): 1656-1676.), I got
confused about van der waals interactions between non-bonded atoms.

for two atom types, we use combination rules to get (Cij 6) and (Cij 12),
and these combination rules (eq. 15 in article) make use of selection
matrix (table 8 in article). However this selection matrix is not
symmetric.

This means L-J interactions between two atom types depends to the order we
put them in [pairs]. Is it correct?

If this is true, then the order of atom numbers in [pair] matters. But it
does not make sense, why (Cij 12) should be different from (Cji 12)?

Thanks in advance for your comments

Best,
Mohsen

--
*Rewards work better than punishment ...*
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Re: [gmx-users] Regarding generating itp file.

[Justin Lemkul]

On 12/11/15 7:01 AM, Raju Lunkad wrote:

Dear GROMACS Admins,

I want to generate itp file of crystal structure ( calcium oxalate
monohyrate). Can anyone  suggest me how to generate itp file.



Ca2+ and water are likely already part of just about any force field.  Oxalate 
is just two carboxylate groups, which is trivial to put together from acid 
building blocks.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Gromacs 5.0.5 Parallelization GPU Tesla S1070

[Antoniel A. S. Gomes]

Hi.

I'm getting another problem using Gromacs in GPU parallelization

I have a Tesla S1070 (T10 Processor) and I'm trying to compile Gromacs 5.0.5 to 
recognize it.

Firstly, let me specify my hardware/software information:

- Ubuntu 14.04 server (no graphical interface)
- Tesla S1070 GPU card (T10 Processor):
 --- PCI bridge: NVIDIA Corporation NF200 PCIe 2.0 switch for Quadro Plex 
S4 / Tesla S870 / Tesla S1070 / Tesla S2050
 --- 3D controller: NVIDIA Corporation GT200GL [Tesla C1060 / M1060]


I tried to follow the suggested tutorials (install nvidia driver, cuda and 
openMM) but mdrun says my card is incompatible, although it's recognized.

I'm afraid if Gromacs 5.0.5 version is able to recognize my GPU card, because 
Tesla S1070 driver (270 version) uses cuda only in 2.2 version (and OpenMM 
needs higher cuda versions).

So, there's a way to configure Tesla S1070 GPU card to get recognized using 
Gromacs 5.0.5? I mean, what drivers versions are needed (or what Gromacs 
versions supports it)?

Best regards,

Antoniel A. S. Gomes

Bacharel em Ciências Biológicas, UEPB - Campus V
Mestre em Biologia Celular e Molecular, UFPB - Campus I
Doutorando em Biologia Geral e Aplicada, UNESP - Instituto de Biociências - 
Botucatu
Lattes: http://lattes.cnpq.br/2330777925652141 
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[gmx-users] [MGMS-DS]: Molecular Modelling Workshop April 4-6, 2016 in Erlangen, Germany

[Harald Lanig]

Dear list subscribers,

I am very happy to announce that the 30th Molecular Modelling Workshop 
in Erlangen takes place on


 April, Monday 4th to Wednesday 6th, 2016.

Starting on Monday after lunch should allow to avoid travelling on 
weekend and keeping the expenses at a minimum. This time, the scientific 
program of the meeting is conducted by Prof. Tim Clark, Technical 
Director of the Computer-Chemistry-Center in Erlangen, Germany. As 
usual, the workshop is organised by the German Section of the Molecular 
Graphics and Modelling Society.


### Plenary Speakers ###
Over the last few decades computational chemistry, molecular modelling, 
and chemoinformatics became more and more an integral part of research 
in various areas of the chemical industry and at universities. A lot of 
new tools and new approaches together with a huge increase in computer 
power facilitate this development.


We are very pleased to announce

Prof. Brian Shoichet
University of California, San Francisco, USA

and

Dr. Marcus A. Neumann
Avant-Garde Materials Simulation Deutschland GmbH

giving plenary presentations as leading experts their respective fields.

### Poster and Lecture Awards ###
As in the past years, there will be two poster awards of EUR 100 each 
and three lecture awards for the best oral presentations:


1st Winner: Travel bursary to attend the Young Modeller's Forum in 
London, UK, plus a speaker slot option at YMF 2016 (travel expenses are 
reimbursed up to EUR 500)

2nd Winner: EUR 200 travel expenses reimbursement
3rd Winner: EUR 100 travel expenses reimbursement

Only undergraduate and graduate research students qualify for the poster 
and lecture awards.


### Registration ###
As every year, an interesting and successful workshop depends on your 
contributions! Therefore let me invite you to submit talks and/or poster 
titles via the registration form accessible on the workshop website


http://mmws2016.mgms-ds.de/index.php?m=register

This website will provide all necessary information about the meeting!
The deadline for all submissions is February 26th, 2016.

+++
Please note that the week before the 30th Molecular Modelling Workshop,

on Wednesday March 30th to Friday April 1st 2016,
a Symposium Commemorating the Life and Work of Paul von Ragué Schleyer

will take place at the same venue. If you are interested in this 
meeting, please follow the link http://schleyersymposium.mgms-ds.de for 
further information.

+++

We are looking forward to meeting you in Erlangen soon!

-Harald Lanig
Chairman of the MGMS-DS e.V.
http://www.mgms-ds.de

--

 PD Dr. Harald Lanig   Universitaet Erlangen/Nuernberg
 Zentralinstitut fuer Scientific Computing (ZISC)
 Geschaeftsfuehrer Martensstrasse 5a, 91058 Erlangen

 Fon   +49 9131-85 20781   harald.la...@fau.de
 Fax   +49 9131-85 20785   http://www.zisc.uni-erlangen.de

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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 140, Issue 43

[Raju Lunkad]

Dear,

In  calcium oxalate monohydrate the charges are,
Type  charge
Ca   2
C 0.992
O(oxal..)  -0.996
O(water)  -0.773
H 0.3665

calcium oxalate monohydrate having two type of bonding which are,
Ox1 oxalate bounded with calcium only
and Ox2, oxalate bounded with calcium and oxygen.So, Kindly help me for
generating itp file for these type of interactions.

On Fri, Dec 11, 2015 at 5:55 PM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:

> Send gromacs.org_gmx-users mailing list submissions to
> gromacs.org_gmx-users@maillist.sys.kth.se
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>
>
> Today's Topics:
>
>1. Re: G53A6, non-symmetric selection metrix (Piggot T.)
>2. Performance on multiple GPUs per node (Jens Kr?ger)
>3. Re: using OH ions in combination with CHARMM27 force  field
>   (soumadwip ghosh)
>4. Re: Performance on multiple GPUs per node (Szil?rd P?ll)
>5. Re: Performance on multiple GPUs per node (Szil?rd P?ll)
>6. Regarding generating itp file. (Raju Lunkad)
>7. Re: Regarding generating itp file. (Justin Lemkul)
>
>
> --
>
> Message: 1
> Date: Fri, 11 Dec 2015 11:12:23 +
> From: "Piggot T." 
> To: "gmx-us...@gromacs.org" 
> Subject: Re: [gmx-users] G53A6, non-symmetric selection metrix
> Message-ID:
> <6989ab580484164ba0a88714dbe8242057c15...@srv00046.soton.ac.uk>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Mohsen,
>
> This table can indeed be quite confusing at first. I suggest you take a
> look at http://redmine.gromacs.org/issues/773#note-10 where there is a
> discussion of how to interpret table 8 (for a specific example, but it
> should highlight how it works). Hopefully that should answer your questions.
>
> Cheers
>
> Tom
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Mohsen
> Ramezanpour [ramezanpour.moh...@gmail.com]
> Sent: 10 December 2015 23:42
> To: Discussion list for GROMACS users
> Subject: [gmx-users] G53A6, non-symmetric selection metrix
>
> Dear All,
>
> Reading the parameters for Gromos 53A6 ff ( article by Oostenbrink  *et al.
> Journal of computational chemistry* 25.13 (2004): 1656-1676.), I got
> confused about van der waals interactions between non-bonded atoms.
>
> for two atom types, we use combination rules to get (Cij 6) and (Cij 12),
> and these combination rules (eq. 15 in article) make use of selection
> matrix (table 8 in article). However this selection matrix is not
> symmetric.
>
> This means L-J interactions between two atom types depends to the order we
> put them in [pairs]. Is it correct?
>
> If this is true, then the order of atom numbers in [pair] matters. But it
> does not make sense, why (Cij 12) should be different from (Cji 12)?
>
> Thanks in advance for your comments
>
> Best,
> Mohsen
>
> --
> *Rewards work better than punishment ...*
> --
> 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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> send a mail to gmx-users-requ...@gromacs.org.
>
> --
>
> Message: 2
> Date: Fri, 11 Dec 2015 11:54:22 +0100
> From: Jens Kr?ger 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Performance on multiple GPUs per node
> Message-ID: <566aab5e.4070...@informatik.uni-tuebingen.de>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Dear all,
>
> we are currently planning a new cluster at our universities compute
> centre. The big question on our side is, how many and which GPUs we
> should put into the nodes.
>
> We have access to a test system with four Tesla K80s per Node. Using one
> GPU node we can reach something like 23 ns/day for the ADH system (PME,
> cubic) which is pretty much in line with e.g.,
> http://exxactcorp.com/index.php/solution/solu_list/84
>
> When trying to use 2 or more GPUs on one node, the performance plunges
> to below 10 ns/day no matter how we split the MPI/OMP threads. Has
> anybody of you guys access to a comparable hardware setup? We would be
> interested in benchmark data answering the 

Re: [gmx-users] Fwd: Help with Gromacs 5.1 mdp options for CHARMM27 force field

[Justin Lemkul]

On 12/11/15 8:49 AM, Rakesh Ramachandran wrote:

Hi Justin,

  Thanks for the reply. Are nstlist and rlist options important for GPU
based gromacs and Verlet cutoff ? I am using nstlist value of 40 and rlist
of 1.2 are these appropriate for CHARMM36.



Verlet tunes both of these as needed.  rlist is automatically adjusted to never 
miss interactions.  The input value is a minimum value; mdrun takes care of the 
rest.



Moreover why is force-switch a better option than other vdw-modifier
options for CHARMM36 ?



This is the method with which the force field was parametrized.  It is 
absolutely required for membrane systems.  Proteins and nucleic acids can be 
debated, but unless you have a rock-solid, verified, reason to change the vdW 
method, don't.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] [gmx-developers] Gromacs 5.0.5 Parallelization GPU Tesla S1070

[Szilárd Páll]

Hi Antoniel,

GROMACS 4.5 should work, just make sure to install a compatible OpenMM
version.

Cheers,

--
Szilárd

On Fri, Dec 11, 2015 at 2:30 PM, Antoniel A. S. Gomes 
wrote:

> Hi Szilárd.
>
> Yeah, I saw that. But the problem is: in gromacs website (
> http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GROMACS-OpenMM)
> says my GPU card is compatible. Probably if I use an older version of
> Gromacs it will works right?
>
> Thank you.
>
> Best regards,
>
> Antoniel A. S. Gomes
>
> Bacharel em Ciências Biológicas, UEPB - Campus V
> Mestre em Biologia Celular e Molecular, UFPB - Campus I
> Doutorando em Biologia Geral e Aplicada, UNESP - Instituto de Biociências
> - Botucatu
> Lattes: http://lattes.cnpq.br/2330777925652141
>
> - Mensagem original -
> De: "Szilárd Páll" 
> Para: "Discussion list for GROMACS users" 
> Enviadas: Sexta-feira, 11 de dezembro de 2015 11:25:33
> Assunto: Re: [gmx-users] [gmx-developers] Gromacs 5.0.5 Parallelization
> GPU Tesla S1070
>
> Hi,
>
> The hardware detection output should clearly state that your GPU is
> incompatible. As the documentation points out [1], only compute capability
> 2.0 or newer GPUs are supported with the CUDA acceleration in GROMACS.
>
>
> http://manual.gromacs.org/documentation/5.1/install-guide/index.html#gpu-support
>
> Cheers,
>
> --
> Szilárd
>
> On Fri, Dec 11, 2015 at 2:01 PM, Antoniel A. S. Gomes  >
> wrote:
>
> > Hi.
> >
> > I'm getting another problem using Gromacs in GPU parallelization
> >
> > I have a Tesla S1070 (T10 Processor) and I'm trying to compile Gromacs
> > 5.0.5 to recognize it.
> >
> > Firstly, let me specify my hardware/software information:
> >
> > - Ubuntu 14.04 server (no graphical interface)
> > - Tesla S1070 GPU card (T10 Processor):
> >  --- PCI bridge: NVIDIA Corporation NF200 PCIe 2.0 switch for Quadro
> > Plex S4 / Tesla S870 / Tesla S1070 / Tesla S2050
> >  --- 3D controller: NVIDIA Corporation GT200GL [Tesla C1060 / M1060]
> >
> >
> > I tried to follow the suggested tutorials (install nvidia driver, cuda
> and
> > openMM) but mdrun says my card is incompatible, although it's recognized.
> >
> > I'm afraid if Gromacs 5.0.5 version is able to recognize my GPU card,
> > because Tesla S1070 driver (270 version) uses cuda only in 2.2 version
> (and
> > OpenMM needs higher cuda versions).
> >
> > So, there's a way to configure Tesla S1070 GPU card to get recognized
> > using Gromacs 5.0.5? I mean, what drivers versions are needed (or what
> > Gromacs versions supports it)?
> >
> > Best regards,
> >
> > Antoniel A. S. Gomes
> >
> > Bacharel em Ciências Biológicas, UEPB - Campus V
> > Mestre em Biologia Celular e Molecular, UFPB - Campus I
> > Doutorando em Biologia Geral e Aplicada, UNESP - Instituto de Biociências
> > - Botucatu
> > Lattes: http://lattes.cnpq.br/2330777925652141
> > --
> > Gromacs Developers mailing list
> >
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> > http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before
> > posting!
> >
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> >
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> > or send a mail to gmx-developers-requ...@gromacs.org.
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[gmx-users] g_membed: how to input position and orientation of a membrane protein into lipid bilayer?

[Rita Melo]

Dear all,

 

I would like to know who have already  used g_membed and where we can define
a specific position and orientation of the membrane protein into lipid
bilayer. I have an issue due TM have a tilt angle of about 34°.

 

Thank you!

Rita.

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Re: [gmx-users] Fwd: Help with Gromacs 5.1 mdp options for CHARMM27 force field

[Rakesh Ramachandran]

Hi Justin,

 Thanks for the reply. Are nstlist and rlist options important for GPU
based gromacs and Verlet cutoff ? I am using nstlist value of 40 and rlist
of 1.2 are these appropriate for CHARMM36.

Moreover why is force-switch a better option than other vdw-modifier
options for CHARMM36 ?

Regards
Rakesh

On 9 December 2015 at 23:27, Justin Lemkul  wrote:

>
>
> On 12/9/15 12:42 PM, Rakesh Ramachandran wrote:
>
>> Hi Justin,
>>
>>   Thanks for the reply. Sorry if this question was too long or I was
>> not
>> clear.
>>
>> 1) What are the optimal values of tau_t and tau_p for CHARMM36. I see
>> in your tutorial that it is 0.1 0.1 for tau_t and 2.0 for tau_p.
>> The CHARMM-GUI generated mdp settings had 1.0 1.0 for tau_t and 5.0 for
>> tau_p. So are higher values more appropriate for CHARMM36 FF and what
>> properties does it effect ?
>>
>>
> Again, to be absolutely clear, values of tau_t and tau_p are in no way
> connected with specific force fields.
>
> The values affect barostat response times and the distributions of
> temperature and pressure values. Too short and the simulations can become
> unstable, too long and the subsequent values may drift a bit before being
> restored. Sometimes longer times are necessary for heterogeneous systems
> like membranes. These are things you must decide based on whatever your
> system is and whatever you find in the literature. I am not going to tell
> you what values you should use.
>
> 3) I was asking Berendsen pressure coupling with respect to the
>> equilibration stage, since I read in some earlier mailing post that
>> Berendsen coupling is more appropriate for temperature (NVT) as well as
>> pressure (NPT) equilibration.
>>
>>
> Yes, for equilibration, Berendsen is often better because it relaxes
> quickly.
>
> 4) Moreover once I do pbc correction I still see one or two ions sticking
>> out of the rhombic dodecahedron box representation in pymol. Is it more of
>> a visualization artifact ?
>>
>>
> Yes, just a visualization artifact.
>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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[gmx-users] water sorient

[xy21hb]

Dear all, I would like to calculate the water orientation near ubiqutin by 
gmx_sorient, gmx sorient -f md.trr -s md.tpr -o -no -ro -co -rc
first, the sord.xvg shows the angle (i.e. theta 1) between the vector1 (nearest 
heavy protein atom to water oxygen) and vector 2 (water oxygen to the mid of of 
water hydrogen 1 and 2) is mostly 90 degrees, isn't that weird?
I would expect water dipole more or less pointing to or away from the vector 1, 
depending on the charge of the heavy atom. 2nd, sori.xvg second column should 
be the distribution of cos (theta1),
but it shows some value greater than 1. Any ideas?

Thanks, Yao
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Re: [gmx-users] [gmx-developers] Gromacs 5.0.5 Parallelization GPU Tesla S1070

[Antoniel A. S. Gomes]

Hi Szilárd.

Yeah, I saw that. But the problem is: in gromacs website 
(http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GROMACS-OpenMM)
 says my GPU card is compatible. Probably if I use an older version of Gromacs 
it will works right?

Thank you.

Best regards,

Antoniel A. S. Gomes

Bacharel em Ciências Biológicas, UEPB - Campus V
Mestre em Biologia Celular e Molecular, UFPB - Campus I
Doutorando em Biologia Geral e Aplicada, UNESP - Instituto de Biociências - 
Botucatu
Lattes: http://lattes.cnpq.br/2330777925652141 

- Mensagem original -
De: "Szilárd Páll" 
Para: "Discussion list for GROMACS users" 
Enviadas: Sexta-feira, 11 de dezembro de 2015 11:25:33
Assunto: Re: [gmx-users] [gmx-developers] Gromacs 5.0.5 Parallelization GPU 
Tesla S1070

Hi,

The hardware detection output should clearly state that your GPU is
incompatible. As the documentation points out [1], only compute capability
2.0 or newer GPUs are supported with the CUDA acceleration in GROMACS.

http://manual.gromacs.org/documentation/5.1/install-guide/index.html#gpu-support

Cheers,

--
Szilárd

On Fri, Dec 11, 2015 at 2:01 PM, Antoniel A. S. Gomes 
wrote:

> Hi.
>
> I'm getting another problem using Gromacs in GPU parallelization
>
> I have a Tesla S1070 (T10 Processor) and I'm trying to compile Gromacs
> 5.0.5 to recognize it.
>
> Firstly, let me specify my hardware/software information:
>
> - Ubuntu 14.04 server (no graphical interface)
> - Tesla S1070 GPU card (T10 Processor):
>  --- PCI bridge: NVIDIA Corporation NF200 PCIe 2.0 switch for Quadro
> Plex S4 / Tesla S870 / Tesla S1070 / Tesla S2050
>  --- 3D controller: NVIDIA Corporation GT200GL [Tesla C1060 / M1060]
>
>
> I tried to follow the suggested tutorials (install nvidia driver, cuda and
> openMM) but mdrun says my card is incompatible, although it's recognized.
>
> I'm afraid if Gromacs 5.0.5 version is able to recognize my GPU card,
> because Tesla S1070 driver (270 version) uses cuda only in 2.2 version (and
> OpenMM needs higher cuda versions).
>
> So, there's a way to configure Tesla S1070 GPU card to get recognized
> using Gromacs 5.0.5? I mean, what drivers versions are needed (or what
> Gromacs versions supports it)?
>
> Best regards,
>
> Antoniel A. S. Gomes
>
> Bacharel em Ciências Biológicas, UEPB - Campus V
> Mestre em Biologia Celular e Molecular, UFPB - Campus I
> Doutorando em Biologia Geral e Aplicada, UNESP - Instituto de Biociências
> - Botucatu
> Lattes: http://lattes.cnpq.br/2330777925652141
> --
> Gromacs Developers mailing list
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> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before
> posting!
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Re: [gmx-users] Regarding generating itp file.

[Justin Lemkul]

Please heed this:

>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of gromacs.org_gmx-users digest..."

...and don't reply to the whole digest.

On 12/11/15 8:02 AM, Raju Lunkad wrote:

Dear,

In  calcium oxalate monohydrate the charges are,
Type  charge
Ca   2
C 0.992
O(oxal..)  -0.996
O(water)  -0.773
H 0.3665

calcium oxalate monohydrate having two type of bonding which are,
Ox1 oxalate bounded with calcium only
and Ox2, oxalate bounded with calcium and oxygen.So, Kindly help me for
generating itp file for these type of interactions.



If you want bonds between those atom types (probably not necessary given the 
strong electrostatic interaction between the carboxylate and Ca2+) you'll have 
to do some sort of QM calculation to get the vibrational frequency and 
subsequently the force constant.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] [gmx-developers] Gromacs 5.0.5 Parallelization GPU Tesla S1070

[Szilárd Páll]

Hi,

The hardware detection output should clearly state that your GPU is
incompatible. As the documentation points out [1], only compute capability
2.0 or newer GPUs are supported with the CUDA acceleration in GROMACS.

http://manual.gromacs.org/documentation/5.1/install-guide/index.html#gpu-support

Cheers,

--
Szilárd

On Fri, Dec 11, 2015 at 2:01 PM, Antoniel A. S. Gomes 
wrote:

> Hi.
>
> I'm getting another problem using Gromacs in GPU parallelization
>
> I have a Tesla S1070 (T10 Processor) and I'm trying to compile Gromacs
> 5.0.5 to recognize it.
>
> Firstly, let me specify my hardware/software information:
>
> - Ubuntu 14.04 server (no graphical interface)
> - Tesla S1070 GPU card (T10 Processor):
>  --- PCI bridge: NVIDIA Corporation NF200 PCIe 2.0 switch for Quadro
> Plex S4 / Tesla S870 / Tesla S1070 / Tesla S2050
>  --- 3D controller: NVIDIA Corporation GT200GL [Tesla C1060 / M1060]
>
>
> I tried to follow the suggested tutorials (install nvidia driver, cuda and
> openMM) but mdrun says my card is incompatible, although it's recognized.
>
> I'm afraid if Gromacs 5.0.5 version is able to recognize my GPU card,
> because Tesla S1070 driver (270 version) uses cuda only in 2.2 version (and
> OpenMM needs higher cuda versions).
>
> So, there's a way to configure Tesla S1070 GPU card to get recognized
> using Gromacs 5.0.5? I mean, what drivers versions are needed (or what
> Gromacs versions supports it)?
>
> Best regards,
>
> Antoniel A. S. Gomes
>
> Bacharel em Ciências Biológicas, UEPB - Campus V
> Mestre em Biologia Celular e Molecular, UFPB - Campus I
> Doutorando em Biologia Geral e Aplicada, UNESP - Instituto de Biociências
> - Botucatu
> Lattes: http://lattes.cnpq.br/2330777925652141
> --
> Gromacs Developers mailing list
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> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before
> posting!
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[gmx-users] parameter for repeating units with cgenff

[gromacs query]

Hi All,

I am using cgenff to derive parameters for some polymer (A-...-C). The
repeating block B has some Oxygen O atom which joins the next residue
(-BO-). When I derive charges for B residue with cgenff then I get net -1
charge on B residue because of this unsatsified O atom. I want to keep B
residue formal charge zero. I get formal charge zero if I derive charges on
B-OH residue but removing H will again will give some non-intergral formal
charge. I am not sure what should done in this regard.

If someone has some experience with this or suggestion I will highly
appreciate it.

Thanks

Jiomm
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Re: [gmx-users] parameter for repeating units with cgenff

[Justin Lemkul]

On 12/11/15 10:17 AM, gromacs query wrote:

Hi All,

I am using cgenff to derive parameters for some polymer (A-...-C). The
repeating block B has some Oxygen O atom which joins the next residue
(-BO-). When I derive charges for B residue with cgenff then I get net -1
charge on B residue because of this unsatsified O atom. I want to keep B
residue formal charge zero. I get formal charge zero if I derive charges on
B-OH residue but removing H will again will give some non-intergral formal
charge. I am not sure what should done in this regard.

If someone has some experience with this or suggestion I will highly
appreciate it.



To derive suitable monomer units, you have to include all the linking atoms; if 
it's an ether of some sort, you need B-O-CH3 or whatever is similar to then 
apply to the actual polymer itself.  Just parametrizing B in the absence of 
flanking atoms is inappropriate.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] AMBER force fields, ff12SB and ff14SB for GROMACS

[Man Hoang Viet]

> Date: Thu, 10 Dec 2015 18:02:32 -0700
> From: Michael Shirts 
> To: Discussion list for GROMACS users 
> Cc: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] AMBER force fields, ff12SB and ff14SB for
>   GROMACS
> Message-ID:
>   
> Content-Type: text/plain; charset=UTF-8
>
> Great!  It's important to have all data validated carefully. Have you
> put together a set of tests, with coverage of all the atom types and
> interaction types, showing that the molecules give the same energies
> in both GROMACS and AMBER?  Validating conversions is quite important
> so that people can trust the results.

I have considered every atoms, atom types, nonbonds and bonds interaction,
atoms in every residues and nucleic acids to make sure they are the same
as in AMBER. If some ones pick up any those things to compare with
original one, I can make sure they will be the same. As you said the test
is very important, but it takes a lot of time and I am working on this. It
will be much better if other gromacs users like you participate the
testing work.

>
> On Thu, Dec 10, 2015 at 4:01 PM, Man Hoang Viet 
> wrote:
>> Dear GROMACS Admins,
>>
>> I have implemented AMBER force field ff12SB and ff14SB into GROMACS and
>> want to share them with all gromacs users. I have tried to upload it via
>> below link
>> http://www.gromacs.org/Downloads/User_contributions/Force_fields
>> However, I can not do register to upload. Could you please tell me how I
>> can share the amber force fields to gromacs users.
>>
>> Thank you very much.
>>
>> Yours sincerely,
>> --
>> Viet Man,
>>
>> Postdoctoral Research Associate,
>> Physics Department, NCSU
>

Viet Man,
Postdoctoral Research Associate,
Physics Department, NCSU

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[gmx-users] Free energy of ice crystals (Thermodynamic Integration)

[Nathan K Houtz]

Hello,


I would like to perform some free energy calculations of ice Ic (cubic ice) at 
various temperatures. However, I'm having difficulty finding information on how 
Gromacs can be used to do this. The goal is to gradually turn off VDW and 
Coulomb interactions, just as one would do in a liquid, but also turn on 
virtual spring-like potentials to create an Einstein crystal, which is where 
I'm having trouble. I know you can fix atom locations, and considering bond 
potentials are spring-like, my best idea is to create a virtual copy of each 
molecule (not virtual sites, but just atoms that have no charge and don't 
interact with other atoms/molecules), fix it in the crystal lattice, and create 
bonds between corresponding atoms with an equilibrium distance of 0. But this 
means I have to simulate twice as many atoms, and more importantly I don't know 
how to couple only some of a molecule's bonds with lambda. Am I even on the 
right track, or is there a more straightforward way to do this? Ar
 e there any tutorials for free energies of solids that I could take a look at? 
(I couldn't find any)


Thanks for your help!

N. H.
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Re: [gmx-users] Free energy of ice crystals (Thermodynamic Integration)

[Michael Shirts]

IF it's NVT, then you should just be able to add harmonic potentials
using the position restraints (not constraints) -- the harmonic
restraints can be controlled by lambda.  You should only need to alter
the charge and VDW interactions -- no need to adjust the bonds.

We have been doing some work on crystals of small organics-- email me
off the list and we might be able to give you some example scripts.

On Fri, Dec 11, 2015 at 8:46 PM, Nathan K Houtz  wrote:
> Hello,
>
>
> I would like to perform some free energy calculations of ice Ic (cubic ice) 
> at various temperatures. However, I'm having difficulty finding information 
> on how Gromacs can be used to do this. The goal is to gradually turn off VDW 
> and Coulomb interactions, just as one would do in a liquid, but also turn on 
> virtual spring-like potentials to create an Einstein crystal, which is where 
> I'm having trouble. I know you can fix atom locations, and considering bond 
> potentials are spring-like, my best idea is to create a virtual copy of each 
> molecule (not virtual sites, but just atoms that have no charge and don't 
> interact with other atoms/molecules), fix it in the crystal lattice, and 
> create bonds between corresponding atoms with an equilibrium distance of 0. 
> But this means I have to simulate twice as many atoms, and more importantly I 
> don't know how to couple only some of a molecule's bonds with lambda. Am I 
> even on the right track, or is there a more straightforward way to do this? 
 Ar
>  e there any tutorials for free energies of solids that I could take a look 
> at? (I couldn't find any)
>
>
> Thanks for your help!
>
> N. H.
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Re: [gmx-users] parameter for repeating units with cgenff

[gromacs query]

Hi Justin

Thanks for the reply. Yes your are right and indeed, sorry I forgot to
mention, I tried with some CH3 and other groups which may be considered as
an appropriate 'cap' which is normally followed by many. But in this case I
will have to remove the cap e.g. B-O-CH3 to B-O- before joining to the next
residue. This causes a net non-integral charge on B-O- which is not correct
as disturbs overall integral charge of the polymer. Ideally the cap once
removed should leave B-O with integral charge. I have tried many caps but
none of them after being removed leave B-O to be integral.


best regards,
Vishal


On Fri, Dec 11, 2015 at 4:43 PM, Justin Lemkul  wrote:

>
>
> On 12/11/15 10:17 AM, gromacs query wrote:
>
>> Hi All,
>>
>> I am using cgenff to derive parameters for some polymer (A-...-C). The
>> repeating block B has some Oxygen O atom which joins the next residue
>> (-BO-). When I derive charges for B residue with cgenff then I get net -1
>> charge on B residue because of this unsatsified O atom. I want to keep B
>> residue formal charge zero. I get formal charge zero if I derive charges
>> on
>> B-OH residue but removing H will again will give some non-intergral formal
>> charge. I am not sure what should done in this regard.
>>
>> If someone has some experience with this or suggestion I will highly
>> appreciate it.
>>
>>
> To derive suitable monomer units, you have to include all the linking
> atoms; if it's an ether of some sort, you need B-O-CH3 or whatever is
> similar to then apply to the actual polymer itself.  Just parametrizing B
> in the absence of flanking atoms is inappropriate.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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> Gromacs Users mailing list
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Re: [gmx-users] G53A6, non-symmetric selection metrix

[Mohsen Ramezanpour]

Thanks Tom!

Got it! now I know how to interpret this table. Great

Cheers
Mohsen



On Fri, Dec 11, 2015 at 4:12 AM, Piggot T.  wrote:

> Hi Mohsen,
>
> This table can indeed be quite confusing at first. I suggest you take a
> look at http://redmine.gromacs.org/issues/773#note-10 where there is a
> discussion of how to interpret table 8 (for a specific example, but it
> should highlight how it works). Hopefully that should answer your questions.
>
> Cheers
>
> Tom
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Mohsen
> Ramezanpour [ramezanpour.moh...@gmail.com]
> Sent: 10 December 2015 23:42
> To: Discussion list for GROMACS users
> Subject: [gmx-users] G53A6, non-symmetric selection metrix
>
> Dear All,
>
> Reading the parameters for Gromos 53A6 ff ( article by Oostenbrink  *et al.
> Journal of computational chemistry* 25.13 (2004): 1656-1676.), I got
> confused about van der waals interactions between non-bonded atoms.
>
> for two atom types, we use combination rules to get (Cij 6) and (Cij 12),
> and these combination rules (eq. 15 in article) make use of selection
> matrix (table 8 in article). However this selection matrix is not
> symmetric.
>
> This means L-J interactions between two atom types depends to the order we
> put them in [pairs]. Is it correct?
>
> If this is true, then the order of atom numbers in [pair] matters. But it
> does not make sense, why (Cij 12) should be different from (Cji 12)?
>
> Thanks in advance for your comments
>
> Best,
> Mohsen
>
> --
> *Rewards work better than punishment ...*
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Re: [gmx-users] parameter for repeating units with cgenff

[Justin Lemkul]

On 12/11/15 12:17 PM, gromacs query wrote:

Hi Justin

Thanks for the reply. Yes your are right and indeed, sorry I forgot to
mention, I tried with some CH3 and other groups which may be considered as
an appropriate 'cap' which is normally followed by many. But in this case I
will have to remove the cap e.g. B-O-CH3 to B-O- before joining to the next
residue. This causes a net non-integral charge on B-O- which is not correct
as disturbs overall integral charge of the polymer. Ideally the cap once
removed should leave B-O with integral charge. I have tried many caps but
none of them after being removed leave B-O to be integral.



Capping groups can't simply be chopped off; that will naturally lead to a 
useless topology.  They need to be designed such that their parameters (charges, 
etc) are analogous to the full-length species such that they can be merged with 
flanking groups.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] parameter for repeating units with cgenff

[gromacs query]

Hi Justin

Thanks for the explanation. Just few things.

1) When you say " Initial charge fitting would be done on a side chain ..."
you mean using some QM method? Which seems expensive and needs expertise
which I dont have.

2) Also, as you said assigning charges and types with analogy does this
mean I can hand pick types and charges looking (carefully) some residues
available with CHARMM and can directly use them? At the same time, then in
this case, I should satisfy the condition of overall integral charge. Am
just wondering in future if reviewer raises question :)


On Fri, Dec 11, 2015 at 6:33 PM, Justin Lemkul  wrote:

>
>
> On 12/11/15 1:28 PM, gromacs query wrote:
>
>> Hi Justin
>>
>> I am bit lost I think. For e.g. in the amino acid residues library we have
>> -CO-CH(R)-NH- which we can combine these amino acids in any way and in the
>> rtp file it defines only these atoms and connecting atoms are mentioned
>> specifically.
>>
>> Now lets say I have some new amino acid -CO-CH(X)-NH- which I want to
>> combine with some existing amino acids. If I want to derive charges from
>> Cgenff what kind of residue I should prepare?
>> Is it NH2-CO-CH(X)-NH-COOH or may be CH3-NH-CO-CH(X)-NH-COCH3. But
>> ultimately I will be requiring only -CO-CH(X)-NH- part. So not considering
>> charges for the caps in topology will give non-integral charge or in other
>> words this part -CO-CH(X)-NH- will always be non-integral. Sorry am
>> confused.
>>
>>
> The backbone group always has a charge of zero, so you only deal with the
> side chain when deriving charges.
>
> Initial charge fitting would be done on a side chain analog that
> terminates in a -CH3 that is analogous to CB.  Once that work is done, the
> model compound is merged with the backbone and CB (which is -CH2, so
> generally the third H charge is just lumped into the C charge) and
> torsional fitting is done for chi1/chi2/etc using a dipeptide model of the
> amino acid.  But at that point the charges are done.
>
> I also wouldn't use CGenFF for a modified amino acid; derive parameters by
> analogy from the parent CHARMM force field.  CGenFF is generalized, at the
> expense of some accuracy.  Mixing CGenFF into a polypeptide chain is not
> the most robust approach.  CHARMM has excellent coverage for most chemical
> moieties.  Simply assigning charges and types by analogy should be quite
> straightforward.
>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
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> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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Re: [gmx-users] parameter for repeating units with cgenff

[Justin Lemkul]

On 12/11/15 2:20 PM, gromacs query wrote:

Hi Justin

Thanks for the explanation. Just few things.

1) When you say " Initial charge fitting would be done on a side chain ..."
you mean using some QM method? Which seems expensive and needs expertise
which I dont have.



Yes, these are generally the initial target data (gas-phase dipole moment, water 
interactions, etc).  Most of these calculations are done by optimizing the 
structure at MP2/6-31G*, which is very straightforward in, e.g. Gaussian.  The 
CGenFF paper has all the details; this is, in essence, what is done for the 
biomolecular CHARMM force field, as well.



2) Also, as you said assigning charges and types with analogy does this
mean I can hand pick types and charges looking (carefully) some residues
available with CHARMM and can directly use them? At the same time, then in
this case, I should satisfy the condition of overall integral charge. Am
just wondering in future if reviewer raises question :)



This is what is generally done.  In fact, this is largely what CGenFF is doing, 
too.  Initial selection of parameters based on rules that reference the library 
of existing compounds.  Refinements are then done based on the initial topology.


-Justin



On Fri, Dec 11, 2015 at 6:33 PM, Justin Lemkul  wrote:




On 12/11/15 1:28 PM, gromacs query wrote:


Hi Justin

I am bit lost I think. For e.g. in the amino acid residues library we have
-CO-CH(R)-NH- which we can combine these amino acids in any way and in the
rtp file it defines only these atoms and connecting atoms are mentioned
specifically.

Now lets say I have some new amino acid -CO-CH(X)-NH- which I want to
combine with some existing amino acids. If I want to derive charges from
Cgenff what kind of residue I should prepare?
Is it NH2-CO-CH(X)-NH-COOH or may be CH3-NH-CO-CH(X)-NH-COCH3. But
ultimately I will be requiring only -CO-CH(X)-NH- part. So not considering
charges for the caps in topology will give non-integral charge or in other
words this part -CO-CH(X)-NH- will always be non-integral. Sorry am
confused.



The backbone group always has a charge of zero, so you only deal with the
side chain when deriving charges.

Initial charge fitting would be done on a side chain analog that
terminates in a -CH3 that is analogous to CB.  Once that work is done, the
model compound is merged with the backbone and CB (which is -CH2, so
generally the third H charge is just lumped into the C charge) and
torsional fitting is done for chi1/chi2/etc using a dipeptide model of the
amino acid.  But at that point the charges are done.

I also wouldn't use CGenFF for a modified amino acid; derive parameters by
analogy from the parent CHARMM force field.  CGenFF is generalized, at the
expense of some accuracy.  Mixing CGenFF into a polypeptide chain is not
the most robust approach.  CHARMM has excellent coverage for most chemical
moieties.  Simply assigning charges and types by analogy should be quite
straightforward.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] parameter for repeating units with cgenff

[gromacs query]

Hi Justin

I am bit lost I think. For e.g. in the amino acid residues library we have
-CO-CH(R)-NH- which we can combine these amino acids in any way and in the
rtp file it defines only these atoms and connecting atoms are mentioned
specifically.

Now lets say I have some new amino acid -CO-CH(X)-NH- which I want to
combine with some existing amino acids. If I want to derive charges from
Cgenff what kind of residue I should prepare?
Is it NH2-CO-CH(X)-NH-COOH or may be CH3-NH-CO-CH(X)-NH-COCH3. But
ultimately I will be requiring only -CO-CH(X)-NH- part. So not considering
charges for the caps in topology will give non-integral charge or in other
words this part -CO-CH(X)-NH- will always be non-integral. Sorry am
confused.

Thanks

On Fri, Dec 11, 2015 at 5:50 PM, Justin Lemkul  wrote:

>
>
> On 12/11/15 12:17 PM, gromacs query wrote:
>
>> Hi Justin
>>
>> Thanks for the reply. Yes your are right and indeed, sorry I forgot to
>> mention, I tried with some CH3 and other groups which may be considered as
>> an appropriate 'cap' which is normally followed by many. But in this case
>> I
>> will have to remove the cap e.g. B-O-CH3 to B-O- before joining to the
>> next
>> residue. This causes a net non-integral charge on B-O- which is not
>> correct
>> as disturbs overall integral charge of the polymer. Ideally the cap once
>> removed should leave B-O with integral charge. I have tried many caps but
>> none of them after being removed leave B-O to be integral.
>>
>>
> Capping groups can't simply be chopped off; that will naturally lead to a
> useless topology.  They need to be designed such that their parameters
> (charges, etc) are analogous to the full-length species such that they can
> be merged with flanking groups.
>
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> 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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Re: [gmx-users] parameter for repeating units with cgenff

[Justin Lemkul]

On 12/11/15 1:28 PM, gromacs query wrote:

Hi Justin

I am bit lost I think. For e.g. in the amino acid residues library we have
-CO-CH(R)-NH- which we can combine these amino acids in any way and in the
rtp file it defines only these atoms and connecting atoms are mentioned
specifically.

Now lets say I have some new amino acid -CO-CH(X)-NH- which I want to
combine with some existing amino acids. If I want to derive charges from
Cgenff what kind of residue I should prepare?
Is it NH2-CO-CH(X)-NH-COOH or may be CH3-NH-CO-CH(X)-NH-COCH3. But
ultimately I will be requiring only -CO-CH(X)-NH- part. So not considering
charges for the caps in topology will give non-integral charge or in other
words this part -CO-CH(X)-NH- will always be non-integral. Sorry am
confused.



The backbone group always has a charge of zero, so you only deal with the side 
chain when deriving charges.


Initial charge fitting would be done on a side chain analog that terminates in a 
-CH3 that is analogous to CB.  Once that work is done, the model compound is 
merged with the backbone and CB (which is -CH2, so generally the third H charge 
is just lumped into the C charge) and torsional fitting is done for 
chi1/chi2/etc using a dipeptide model of the amino acid.  But at that point the 
charges are done.


I also wouldn't use CGenFF for a modified amino acid; derive parameters by 
analogy from the parent CHARMM force field.  CGenFF is generalized, at the 
expense of some accuracy.  Mixing CGenFF into a polypeptide chain is not the 
most robust approach.  CHARMM has excellent coverage for most chemical moieties. 
 Simply assigning charges and types by analogy should be quite straightforward.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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