[gmx-users] gromacs.org_gmx-users Digest, Vol 129, Issue 32
asasa qsqs
sanaz_dr_m at yahoo.com
Fri Jan 9 08:42:50 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 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
gromacs.org_gmx-users at maillist.sys.kth.se
To subscribe or unsubscribe via the World Wide Web, visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
or, via email, send a message with subject or body 'help' to
gromacs.org_gmx-users-request at maillist.sys.kth.se
You can reach the person managing the list at
gromacs.org_gmx-users-owner at maillist.sys.kth.se
When replying, please edit your Subject line so it is more specific
than "Re: Contents of gromacs.org_gmx-users digest..."
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>
------------------------------
--
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.
End of gromacs.org_gmx-users Digest, Vol 129, Issue 32
******************************************************
More information about the gromacs.org_gmx-users
mailing list