hello everyone
ok justin but i used DSTRONG_POSERES in topology not the STRONG_POSERES
and -DSTRONG_POSERES
ok i will try to send the image
kindly check my tolpology is it ok
thanks in advance
On Fri, Jul 18, 2014 at 4:10 PM, Justin Lemkul wrote:
>
>
> On 7/18/14, 3:34 AM, RINU KHATTRI wrote:
>
Hi dear Gromacs users, i would like to report something maybe could be a
bug or a mistake of me , you´ll see, i run an MD of a System with CNT
Protein Water and ions, i use a index.ndx file, my CNT doestn´t have any
charges, but when i check the Coul SR CNT-CNT there were really huge,
so i start
Hello GROMACS users,
I am just wondering wether there is significant difference in performance
between GROMACS on over clocked CPU vs GROMACS on non clocked CPU? Is possible
to over clocked CPU on GROMACS. This is important for me as i am going to build
a computer with or without over clocking
On Fri, Jul 18, 2014 at 8:54 PM, Yunlong Liu wrote:
> Hi Szilard,
>
> Thank you for your comments.
> I really learn a lot from that. Can you please explain more on the -nb
> gpu_cpu tag?
It's a command line option that tells mdrun to use the hybrid mode in
which the loncal non-bonded interaction
Hi Szilard,
Thank you for your comments.
I really learn a lot from that. Can you please explain more on the -nb gpu_cpu
tag?
And what I know is the Stampede node contains 16 Intel Xeon cores with only one
Tesla K20m GPU. But you mention there are two CPU XEON cores. I am a little
confused on th
On Fri, Jul 18, 2014 at 8:25 PM, Yunlong Liu wrote:
> Hi Mark,
>
> I post up my log file for the run here. Thank you.
>
> Log file opened on Wed Jul 16 11:26:51 2014
> Host: c442-403.stampede.tacc.utexas.edu pid: 31032 nodeid: 0 nnodes: 4
> GROMACS:mdrun_mpi_gpu, VERSION 5.0-rc1
>
> GROMAC
On Fri, Jul 18, 2014 at 7:31 PM, Yunlong Liu wrote:
> Hi,
>
> Thank you for your reply.
> I am actually not doing anything unusual, just common MD simulation of a
> protein. My system contains ~25 atoms, more or less depend on how many
> water molecules I put in it.
>
> The way I called mdru
Hi Mark,
I post up my log file for the run here. Thank you.
Log file opened on Wed Jul 16 11:26:51 2014
Host: c442-403.stampede.tacc.utexas.edu pid: 31032 nodeid: 0 nnodes: 4
GROMACS:mdrun_mpi_gpu, VERSION 5.0-rc1
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. B
hi, I am simulating carbon nanotubes in gromacs. I am preparing my
forcefield.itp file and i want to use the twofold cosine torsion as my
dihedraltype. The form of the potential i want use is -
0.5 * K_cphi*(1- cos(2*phi_ijkl))
I have 2 questions regarding this.
1. I saw the chapter 4 in the man
Hi,
Thank you for your reply.
I am actually not doing anything unusual, just common MD simulation of a
protein. My system contains ~25 atoms, more or less depend on how many
water molecules I put in it.
The way I called mdrun is
ibrun mdrun_mpi_gpu -pin on -ntomp 8 -deffnm pi3k-wt-1 -gpu_i
Hi dear gromacs Users
I am dealing with a Coul SR energy problem, my system has an CNT , Water,
Ions , POPC and an ION CHANNEL, i have already equilibrating, the
Temperature and Pressure are OK, but when i run 10ns of MD, my Coul SR
CNT-CNT is really big,
Energy Avera
Dear All,
I am running simulations of BMP2 protein and graphite sheet using implicit
solvent model (mdp file is pasted below). The graphite atoms are frozen in the
simulation and BMP2 is free to translate.
I got an error "Step 1786210: The domain decomposition grid has shifted too
much in the Z
Hi,
That's highly unusual, and suggests you are doing something highly unusual,
like trying to run on huge numbers of threads, or very large numbers of
bonded interactions. How are you setting up to call mdrun, and what is in
your tpr?
Mark
On Jul 17, 2014 10:13 PM, "Yunlong Liu" wrote:
> Hi,
>
On 7/18/14, 7:28 AM, Yana Tsoneva wrote:
Dear colleagues,
I am dealing with systems consisting of water/different oils. I am
using Gromacs-4.6.5. I have wrote to You twice about my problems (You can
find my previous messages and their answers below), but I still can not deal
with them.
Unt
On 7/18/14, 11:19 AM, Tom wrote:
Dear Gromacs,
i have a set of amber force field parameter from literature.
i have to convert them into gromacs.
i am wondering if there is any spreadsheet available to
do this manual conversion to prevent any mistake.
I don't know about spreadsheets, but co
On 7/18/14, 11:34 AM, sjub...@purdue.edu wrote:
Hi,
I am a new Gromacs user, and while I've been following the KALP-15 in DPPC
tutorial, I seem to have hit a snag.
1. After the step where I manually edited the topology file and created the
gromos53a6_lipid forcefield directory, I tried to con
Hi,
I am a new Gromacs user, and while I've been following the KALP-15 in DPPC
tutorial, I seem to have hit a snag.
1. After the step where I manually edited the topology file and created the
gromos53a6_lipid forcefield directory, I tried to convert the dppc128.pdb file
to .gro format using
Dear Gromacs,
i have a set of amber force field parameter from literature.
i have to convert them into gromacs.
i am wondering if there is any spreadsheet available to
do this manual conversion to prevent any mistake.
thanks!
Thom
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On Jul 17, 2014, at 15:10, Nizar wrote:
>
>
> On Jul 14, 2014, at 15:57, Mirco Wahab
> wrote:
>
>> On 14.07.2014 10:21, Nizar wrote:
>>> Can I force GROMACS 5.0 to use both CPU and GPU?
>>
Afaik unfortunately not.
>
>> I thought it could be forced as GROMACS 4.5.x did
>>
>>> I s
On Jul 17, 2014, at 15:10, Nizar wrote:
>
>
> On Jul 14, 2014, at 15:57, Mirco Wahab
> wrote:
>
>> On 14.07.2014 10:21, Nizar wrote:
>>> Can I force GROMACS 5.0 to use both CPU and GPU?
>>
Afaik unfortunately not.
>
>> I thought it could be forced as GROMACS 4.5.x did
>>
>>> I s
Dear colleagues,
I am dealing with systems consisting of water/different oils. I am
using Gromacs-4.6.5. I have wrote to You twice about my problems (You can
find my previous messages and their answers below), but I still can not deal
with them.
Until now I ran my simulations with TIP4P wat
On 7/18/14, 6:38 AM, RINU KHATTRI wrote:
hello every one
i am still in minimization step i thing i notice is -DSTRONG_POSERES is not
working even i added DSTRONG_POSERES in topology file
Because you've made a typo. -DSTRONG_POSERES will not trigger the STRONG_POSRES
block.
-Justin
i sim
On 7/18/14, 3:34 AM, RINU KHATTRI wrote:
hello justin images can not be sent by this email address (gmx--) i am
helpless how can i send it to you (protein is out side the lipid membrane )
thank you
Upload images to a file-sharing service and post the links to the images.
-Justin
On Fri,
hello every one
i am still in minimization step i thing i notice is -DSTRONG_POSERES is not
working even i added DSTRONG_POSERES in topology file
i simpley used DPOSERES it workks in log file value is there
Energies (kJ/mol)
BondG96Bond Angle G96AngleProper Dih
Hi, I know certain functional forms are represented by certain integers in the
.itp files. As I’m constructing my own .itp file, I wish to know where is a
possible place for me to find out which integer represents which functional
form?
Thanks, any help is greatly appreciated. =)
Yip Yew Mun (
Hi,
Have you fixed the problem?
On BG/Q, Version 4.6.5.
Here, the /libmass_simd.a is under /opt/ibmcmp/xlmass/bg/7.3/bglib64
(it may different from yours).
During cmake I added
-DCMAKE_C_FLAGS="-O3 -L/opt/ibmcmp/xlmass/bg/7.3/bglib64 -lmass_simd"
It works on my side, you may do a check by yo
hello justin images can not be sent by this email address (gmx--) i am
helpless how can i send it to you (protein is out side the lipid membrane )
thank you
On Fri, Jul 18, 2014 at 1:01 PM, RINU KHATTRI
wrote:
> hello gromacs users
> i saw my em.log file after minimization no position restrain
hello gromacs users
i saw my em.log file after minimization no position restrain term is there
even i used -D flag
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Strong position restraints for InflateGRO
#ifdef -DSTRONG_POSRES
#include "strong_posre.itp"
#endif
; St
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