[gmx-users] GridMAT-MD

Fri Jan 9 09:48:19 CET 2015

Dear Justin,I want to use?GridMAT-MD program?for last 70 ns my simulation, wat must i do?Many thanks,Mrs. Mahdavi 

     On Friday, January 9, 2015 11:13 AM, "gromacs.org_gmx-users-request at maillist.sys.kth.se" <gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

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Today's Topics:

  1. Re: RDF plot with large g(r) values (Kester Wong)
  2.  Changing number of processors after a job restart (Nash, Anthony)
  3. Re: gromacs.org_gmx-users Digest, Vol 129, Issue 32 (asasa qsqs)

----------------------------------------------------------------------

Message: 1
Date: Fri, 9 Jan 2015 11:34:19 +0900
From: Kester Wong <Kester2014 at ibs.re.kr>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] RDF plot with large g(r) values
Message-ID: <Mime4j.5c68.3e3961f276b100ed.14acc8ad8d6 at ibs.re.kr>
Content-Type: text/plain; charset="us-ascii"

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Message: 2
Date: Fri, 9 Jan 2015 07:00:34 +0000
From: "Nash, Anthony" <a.nash at ucl.ac.uk>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Subject: [gmx-users]  Changing number of processors after a job
    restart
Message-ID:
    <DB3PR01MB07640FBCBD559FBF07F00392C7440 at DB3PR01MB0764.eurprd01.prod.exchangelabs.com>

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Hi all,

This is probably quite a fundamental bit of knowledge I am missing (and struggling to find). In an effort to just get a system running rather than waiting on a queue I am considering taking my job which has already ran for 48 hours and reducing the requested number of nodes. I would use the usual -cpi ----.cpt -noappend notation in the job script to resubmit.

I have a feeling though, that all manor of parallel calculations were preserved in the check point file and are loaded upon restart. Would my job reload and recalculate all the relevant cell decomposition, etc., without throwing up an error.

Many thanks
Anthony 

------------------------------

Message: 3
Date: Fri, 9 Jan 2015 07:42:42 +0000 (UTC)
From: asasa qsqs <sanaz_dr_m at yahoo.com>
To: "gromacs.org_gmx-users at maillist.sys.kth.se"
    <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 129, Issue
    32
Message-ID:
    <644329394.987672.1420789362616.JavaMail.yahoo at jws106125.mail.bf1.yahoo.com>

Content-Type: text/plain; charset=UTF-8

Dear Justin,I want to use?GridMAT-MD program?for last 70 ns my simulation, wat must i do?Many thanks,Mrs. Mahdavi 

    On Friday, January 9, 2015 5:21 AM, "gromacs.org_gmx-users-request at maillist.sys.kth.se" <gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

 Send gromacs.org_gmx-users mailing list submissions to
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Today's Topics:

? 1. Re: Error : Atomtype not found (Justin Lemkul)
? 2. rotating triclinic box (felipe zapata)
? 3. Re: rotating triclinic box (Tsjerk Wassenaar)
? 4. compiling issue (?ric Germaneau)
? 5. Re: compiling issue (?ric Germaneau)
? 6. Re: RDF plot with large g(r) values (Kester Wong)

----------------------------------------------------------------------

Message: 1
Date: Thu, 08 Jan 2015 10:27:26 -0500
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Error : Atomtype not found
Message-ID: <54AEA1DE.6020403 at vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

On 1/8/15 10:14 AM, protim chakraborti wrote:
> Respected Dr. Lemkul
> Thanks for the suggestion. I have checked the ffnonbonded.itp and found
> that copper is entered out there in the following form and format
>
> ; Ions and noble gases (useful for tutorials)
> Cu2+? ? 29? ? ? 63.54600? ? ? ? 2.00? ? A? ? ? 2.08470e-01? ? 4.76976e+00
> Ar? ? ? 18? ? ? 39.94800? ? ? ? 0.00? ? A? ? ? 3.41000e-01? ? 2.74580e-02
>
> would this be not be suffice or i need to add Cu separately? or may be I
> have to run starting from pdb2gmx itself!
>

Those parameters are not CHARMM parameters.? They appear to have been copied 
over from OPLS-AA, which had several ions removed due to unknown origins (as was 
Ar).? Do not use these parameters for a CHARMM simulation.? I recommend that 
they be removed entirely, as we did with our CHARMM36 port.

-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

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

==================================================

------------------------------

Message: 2
Date: Thu, 8 Jan 2015 16:25:03 -0500
From: felipe zapata <tifonzafel at gmail.com>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] rotating triclinic box
Message-ID:
??? <CA+AeLgSe5Pj8iRcgaFU9-E4zx7830PK9p=OatuuDnFa9zrmg-w at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi all,
I have a triclinic box containing several chains of a biopolymer with the
following crystal information:

CRYST1? 115.000? 75.000? 75.000? 80.37 118.08 114.80 P 1? ? ? ? ? 1

I want to apply a semiistropic pressure coupling orthogonal to the chains
(XY plane), but unfortunately the strands of the polymer are oriented along
the x-axis instead of the z-axis. How can I change the orientation of the
box in such a way that the strand are orientated along the z-axis? it means
I want to rotate the triclinic box swapping the x and z axes.

Best,

Felipe

------------------------------

Message: 3
Date: Thu, 8 Jan 2015 22:39:03 +0100
From: Tsjerk Wassenaar <tsjerkw at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Subject: Re: [gmx-users] rotating triclinic box
Message-ID:
??? <CABzE1SjRMvh-HgWDRtnk_GKrS3_f5moPcL1K3dce+Qrt79SMhA at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

Hi Felipe,

Rotate 90 degrees around y:

editconf -rotate 0 90 0

Cheers,

Tsjerk
On Jan 8, 2015 10:32 PM, "felipe zapata" <tifonzafel at gmail.com> wrote:

> Hi all,
> I have a triclinic box containing several chains of a biopolymer with the
> following crystal information:
>
> CRYST1? 115.000? 75.000? 75.000? 80.37 118.08 114.80 P 1? ? ? ? ? 1
>
> I want to apply a semiistropic pressure coupling orthogonal to the chains
> (XY plane), but unfortunately the strands of the polymer are oriented along
> the x-axis instead of the z-axis. How can I change the orientation of the
> box in such a way that the strand are orientated along the z-axis? it means
> I want to rotate the triclinic box swapping the x and z axes.
>
> Best,
>
> Felipe
> --
> 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-request at gromacs.org.
>

------------------------------

Message: 4
Date: Fri, 09 Jan 2015 08:21:09 +0800
From: ?ric Germaneau <germaneau at sjtu.edu.cn>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Subject: [gmx-users] compiling issue
Message-ID: <54AF1EF5.7040208 at sjtu.edu.cn>
Content-Type: text/plain; charset=utf-8; format=flowed

Dear all,

I'm trying to build GMX on a Intel CentOS release 6.6 machine using icc 
14.0 and CUDA 6.5.
Here are the error I get:

? ? [? 1%] Built target mdrun_objlib
? ? In file included from /usr/local/cuda/include/crt/device_runtime.h(251),
? ? ? ? ? ? ? ? ? ? ? from
? ? /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h(212):
? ? /usr/local/cuda/include/crt/storage_class.h(61): remark #7:
? ? unrecognized token
? ? ? #define __storage_auto__device__ @@@ COMPILER @@@ ERROR @@@

? ? ...//

? ? /usr/local/cuda/include/crt/host_runtime.h(121): remark #82: storage
? ? class is not first
? ? ? static void ____nv_dummy_param_ref(void *param) { volatile static
? ? void * *__ref __attribute__((unused)); __ref = (volatile void *
? ? *)param; }

? ? ...

? ? Scanning dependencies of target cuda_tools
? ? Linking CXX static library ../../../../lib/libcuda_tools.a
? ? [? 1%] Built target cuda_tools
? ? [? 2%] [? 2%] Building NVCC (Device) object
? ? src/gromacs/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir/nbnxn_cuda_generated_nbnxn_cuda_data_mgmt.cu.o
? ? Building NVCC (Device) object
? ? src/gromacs/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir/nbnxn_cuda_generated_nbnxn_cuda.cu.o
? ? /usr/local/cuda/include/crt/host_runtime.h(121): remark #82: storage
? ? class is not first
? ? ? static void ____nv_dummy_param_ref(void *param) { volatile static
? ? void * *__ref __attribute__((unused)); __ref = (volatile void *
? ? *)param;

? ? ...

? ? /tmp/iccZVwEChas_.s: Assembler messages:
? ? /tmp/iccZVwEChas_.s:375: Error: suffix or operands invalid for `vpaddd'
? ? /tmp/iccZVwEChas_.s:467: Error: no such instruction: `vpbroadcastd
? ? %xmm0,%ymm0'
? ? /tmp/iccZVwEChas_.s:628: Error: suffix or operands invalid for `vpxor'
? ? /tmp/iccZVwEChas_.s:629: Error: suffix or operands invalid for
? ? `vpcmpeqd'
? ? /tmp/iccZVwEChas_.s:630: Error: no such instruction: `vpbroadcastd
? ? %xmm0,%ymm0'
? ? /tmp/iccZVwEChas_.s:709: Error: suffix or operands invalid for
? ? `vpcmpeqd'
? ? /tmp/iccZVwEChas_.s:711: Error: suffix or operands invalid for `vpxor'
? ? /tmp/iccZVwEChas_.s:712: Error: suffix or operands invalid for `vpsubd'
? ? /tmp/iccZVwEChas_.s:713: Error: suffix or operands invalid for `vpaddd'
? ? /tmp/iccZVwEChas_.s:1620: Error: no such instruction: `shlx
? ? %r8d,%eax,%r11d'
? ? /tmp/iccZVwEChas_.s:2000: Error: no such instruction: `shlx
? ? %r8d,%eax,%r10d'
? ? /tmp/iccZVwEChas_.s:2107: Error: no such instruction: `shlx
? ? %r9d,%eax,%eax'
? ? /tmp/iccZVwEChas_.s:2485: Error: suffix or operands invalid for `vpaddd'
? ? /tmp/iccZVwEChas_.s:3255: Error: suffix or operands invalid for `vpaddd'
? ? /tmp/iccZVwEChas_.s:3650: Error: suffix or operands invalid for `vpaddd'
? ? /tmp/iccZVwEChas_.s:4154: Error: suffix or operands invalid for `vpaddd'
? ? CMake Error at gpu_utils_generated_memtestG80_core.cu.o.cmake:264
? ? (message):
? ? ? Error generating file
? ? /home/eric/soft/science/opensource/gromacs/build-5.0.4/src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_memtestG80_core.cu.o

? ? make[2]: ***
? ? [src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/gpu_utils_generated_memtestG80_core.cu.o]
? ? Error 1
? ? make[1]: ***
? ? [src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/all] Error 2
? ? make: *** [all] Error 2

The CPU version compile smoothly.
Any hint here ?

? ? ?ric.

-- 
?ric Germaneau (???), Specialist
Center for High Performance Computing
Shanghai Jiao Tong University
Room 205 Network Center, 800 Dongchuan Road, Shanghai 200240 China
M:germaneau at sjtu.edu.cn P:+86-136-4161-6480 W:http://hpc.sjtu.edu.cn

------------------------------

Message: 5
Date: Fri, 09 Jan 2015 08:22:59 +0800
From: ?ric Germaneau <germaneau at sjtu.edu.cn>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Subject: Re: [gmx-users] compiling issue
Message-ID: <54AF1F63.5010800 at sjtu.edu.cn>
Content-Type: text/plain; charset=utf-8; format=flowed

So sorry, I forgot to mention I use *GMX 5.0.4*.

On 01/09/2015 08:21 AM, ?ric Germaneau wrote:
> Dear all,
>
> I'm trying to build GMX on a Intel CentOS release 6.6 machine using 
> icc 14.0 and CUDA 6.5.
> Here are the error I get:
>
>? ? [? 1%] Built target mdrun_objlib
>? ? In file included from 
> /usr/local/cuda/include/crt/device_runtime.h(251),
>? ? ? ? ? ? ? ? ? ? ? from
>? ? /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h(212):
>? ? /usr/local/cuda/include/crt/storage_class.h(61): remark #7:
>? ? unrecognized token
>? ? ? #define __storage_auto__device__ @@@ COMPILER @@@ ERROR @@@
>
>? ? ...//
>
>? ? /usr/local/cuda/include/crt/host_runtime.h(121): remark #82: storage
>? ? class is not first
>? ? ? static void ____nv_dummy_param_ref(void *param) { volatile static
>? ? void * *__ref __attribute__((unused)); __ref = (volatile void *
>? ? *)param; }
>
>? ? ...
>
>? ? Scanning dependencies of target cuda_tools
>? ? Linking CXX static library ../../../../lib/libcuda_tools.a
>? ? [? 1%] Built target cuda_tools
>? ? [? 2%] [? 2%] Building NVCC (Device) object
> src/gromacs/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir/nbnxn_cuda_generated_nbnxn_cuda_data_mgmt.cu.o
>? ? Building NVCC (Device) object
> src/gromacs/mdlib/nbnxn_cuda/CMakeFiles/nbnxn_cuda.dir/nbnxn_cuda_generated_nbnxn_cuda.cu.o
>? ? /usr/local/cuda/include/crt/host_runtime.h(121): remark #82: storage
>? ? class is not first
>? ? ? static void ____nv_dummy_param_ref(void *param) { volatile static
>? ? void * *__ref __attribute__((unused)); __ref = (volatile void *
>? ? *)param;
>
>? ? ...
>
>? ? /tmp/iccZVwEChas_.s: Assembler messages:
>? ? /tmp/iccZVwEChas_.s:375: Error: suffix or operands invalid for 
> `vpaddd'
>? ? /tmp/iccZVwEChas_.s:467: Error: no such instruction: `vpbroadcastd
>? ? %xmm0,%ymm0'
>? ? /tmp/iccZVwEChas_.s:628: Error: suffix or operands invalid for `vpxor'
>? ? /tmp/iccZVwEChas_.s:629: Error: suffix or operands invalid for
>? ? `vpcmpeqd'
>? ? /tmp/iccZVwEChas_.s:630: Error: no such instruction: `vpbroadcastd
>? ? %xmm0,%ymm0'
>? ? /tmp/iccZVwEChas_.s:709: Error: suffix or operands invalid for
>? ? `vpcmpeqd'
>? ? /tmp/iccZVwEChas_.s:711: Error: suffix or operands invalid for `vpxor'
>? ? /tmp/iccZVwEChas_.s:712: Error: suffix or operands invalid for 
> `vpsubd'
>? ? /tmp/iccZVwEChas_.s:713: Error: suffix or operands invalid for 
> `vpaddd'
>? ? /tmp/iccZVwEChas_.s:1620: Error: no such instruction: `shlx
>? ? %r8d,%eax,%r11d'
>? ? /tmp/iccZVwEChas_.s:2000: Error: no such instruction: `shlx
>? ? %r8d,%eax,%r10d'
>? ? /tmp/iccZVwEChas_.s:2107: Error: no such instruction: `shlx
>? ? %r9d,%eax,%eax'
>? ? /tmp/iccZVwEChas_.s:2485: Error: suffix or operands invalid for 
> `vpaddd'
>? ? /tmp/iccZVwEChas_.s:3255: Error: suffix or operands invalid for 
> `vpaddd'
>? ? /tmp/iccZVwEChas_.s:3650: Error: suffix or operands invalid for 
> `vpaddd'
>? ? /tmp/iccZVwEChas_.s:4154: Error: suffix or operands invalid for 
> `vpaddd'
>? ? CMake Error at gpu_utils_generated_memtestG80_core.cu.o.cmake:264
>? ? (message):
>? ? ? Error generating file
> /home/eric/soft/science/opensource/gromacs/build-5.0.4/src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_memtestG80_core.cu.o
>
>
>? ? make[2]: ***
> [src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/gpu_utils_generated_memtestG80_core.cu.o]
>? ? Error 1
>? ? make[1]: ***
>? ? [src/gromacs/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/all] Error 2
>? ? make: *** [all] Error 2
>
> The CPU version compile smoothly.
> Any hint here ?
>
>? ? ?ric.
>

-- 
?ric Germaneau (???), Specialist
Center for High Performance Computing
Shanghai Jiao Tong University
Room 205 Network Center, 800 Dongchuan Road, Shanghai 200240 China
M:germaneau at sjtu.edu.cn P:+86-136-4161-6480 W:http://hpc.sjtu.edu.cn

------------------------------

Message: 6
Date: Fri, 9 Jan 2015 10:49:46 +0900
From: Kester Wong <Kester2014 at ibs.re.kr>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] RDF plot with large g(r) values
Message-ID: <Mime4j.5c0d.cc66669f8e8d4fb1.14acc621173 at ibs.re.kr>
Content-Type: text/plain; charset="us-ascii"

An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20150109/33589613/attachment.html>

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