Dear sir,
i have running new molecules add in standard protein that new is
morin molecules unfortunetly 102 error occur
which is no defualt angle found , etc. i overcome this problem but one more
new appear which is shown below
could you help me to overcome these following errror
26 atoms ar
Dear All,
For the MD extension purpose by "mdrun -s OUT_PUT.tpr -cpi md-0-1_prev.cpt" as
discussed in the following e-mail, will you please tell me the difference
between md-0-1_prev.cpt and md-0-1.cpt?
I want to know the difference enven minor.
I am looking forward to getting your reply.
Ch
Hi Acoot,
Better to use the following command
tpbconv -s md-0-1.tpr -extend (PUT HOW LONG YOU WANT TO RUN IN ps HERE) -o
OUT_PUT.tpr
mdrun -s OUT_PUT.tpr -cpi md-0-1_prev.cpt
You have to use your own proper naming and do not forget to put how long you
should extend it in picosecond (for examp
Dear All,
I have run a 5 ns MD by
mdrun -deffnn md-0-1
After about 1 ns the computer was out of power by accident. I tried to continue
run the MD. From the on-line material there is a method "mdrun -s topol.tpr
-cpi state.cpt".
But by the above mdrun -deffnn md-0-1, I find I got 2 cpt files,
Again I will remind you to keep all Gromacs-related correspondence on the
gmx-users list. I am CC'ing the list and expect that all future questions and
discussion will be posted there.
On 2/5/13 9:52 PM, Arunima Shilpi wrote:
Hello sir
I would like to know how do we rectify the charges of
On Tue, Feb 5, 2013 at 10:05 PM, S. Alireza Bagherzadeh <
s.a.bagherzade...@gmail.com> wrote:
> Hi everyone,
>
> I am using "editconf" to translate my system along the z-axis.
>
Why? mdrun doesn't care.
However, by trial and error I realized that only at some values of the
> z-component of the t
On 2/5/13 10:44 AM, vidhya sankar wrote:
Dear Justin Thank you for your Previous reply,
I
am following your Protein -Lipid tutorial . I am doing simulation of Assembly
of Cyclic Peptide
( Made up of Only Phenyl a
g_select can do it. E.g.:
g_select -f out.gro -s topol.tpr -n index.ndx -select '"solvation_shell"
resname SOL and within 0.4 of group "SOLUTE"' -on shell.ndx
might work
Javier
El 05/02/13 18:54, Dr. Vitaly Chaban escribió:
Could anyone please remind me the name of the utility, which genera
> Date: Mon, 04 Feb 2013 15:32:17 -0500
> From: Justin Lemkul
> Subject: Re: [gmx-users] gromacs-4.6.tar.gz installation question
> To: Discussion list for GROMACS users
> Message-ID: <51101ad1.3000...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 2/4/13 3:30 PM
On 2/5/13 9:04 AM, Arunima Shilpi wrote:
Dear Sir/ Madam
I am using gromacs for simulation and has the following while running the command for
"grompp"
Expected integer argument for option -maxwarn "".
I do not want use maxwarn to bypass the error.
I request you to kindly help me out to deb
Dear Justin Thank you for your Previous reply,
I
am following your Protein -Lipid tutorial . I am doing simulation of Assembly
of Cyclic Peptide
( Made up of Only Phenyl alanine Residue) in DPPC lipid
On Tue, Feb 5, 2013 at 8:58 AM, Berk Hess wrote:
>
> One last thing:
> Maybe a macro is not set, but we can actually query the number of
> processors.
> Could you replace the conditional that gets triggered on my machine:
> #if defined(_SC_NPROCESSORS_ONLN)
> to
> #if 1
>
> So we can check if the
Mark,
Thank you for your answer.
I have already tried to run with several numbers of processors from 8 to
512 and I always got the same error.
And I transfer the simulation to the BlueGene in two different ways. In
both ways, I got the same error.
They were the following:
1) only using the
Hi, Joakim-
Expanded ensemble is still a bit experimental. I don't immediately
see any problem that jump right out, but if you go to
http://redmine.gromacs.org/ and file a bug report, including giving
example files that cause the problem, I can take a look at it.
On Tue, Feb 5, 2013 at 6:00 AM,
Dear Sir/ Madam
I am using gromacs for simulation and has the following while running the
command for "grompp"
Expected integer argument for option -maxwarn "".
I do not want use maxwarn to bypass the error.
I request you to kindly help me out to debug the error.
Regards
Arunima
--
gmx-users
One last thing:
Maybe a macro is not set, but we can actually query the number of processors.
Could you replace the conditional that gets triggered on my machine:
#if defined(_SC_NPROCESSORS_ONLN)
to
#if 1
So we can check if the actual sysconf call works or not?
My workaround won't work without
Head of .log:
Gromacs version:VERSION 5.0-dev-20121213-e1fcb0a-dirty
GIT SHA1 hash: e1fcb0a3d2768a8bb28c2e4e8012123ce773e18c (dirty)
Precision: single
MPI library:MPI
OpenMP support: disabled
GPU support:disabled
invsqrt routine:gmx_software_invsqrt(x)
CPU
On Mon, Feb 4, 2013 at 5:18 PM, Cintia C. Vequi-Suplicy wrote:
>
>
>
> Hello David,
>
> I think it is the pressure.
>
I would think the mentions of pressure are just one of the symptoms. See
http://www.gromacs.org/Documentation/Terminology/Blowing_Up.
You seem to have somewhat more than 100K ato
On 2/5/13 2:10 AM, az kalsom wrote:
hi,
i wanted to say i am not able to make acpype for me, i am following the
tutorial , http://code.google.com/p/acpype/wiki/HowToUse
but i am still geeting the error that this comand is not found
anybody please help me
It's just a Python script, so you c
On 2/4/13 11:09 PM, John K wrote:
Hello Justin,
Thank you for providing a tutorial for membrane simulation.
I am doing membrane simulation by following your tutorial.
When I tried to do energy minimization after inflating the system i got the
following result.
Steepest Descents converged to m
OK, then this is an unhandled case.
Strange, because I am also running OpenSUSE 12.2 with the same CPU, but use gcc
4.7.1.
I will file a bug report on redmine.
Could you also post the header of md.log which gives all configuration
information?
To make it work for now, you can insert immediate
None of the variables referenced here are set on my system, the print
statements are never executed.
What I did:
printf("Checking which processor variable is set");
#if defined(_SC_NPROCESSORS_ONLN)
ret = sysconf(_SC_NPROCESSORS_ONLN);
printf("case 1 ret = %d\n",ret);
#elif defined(_SC_N
Hi,
This is the same cpu I have in my workstation and this case should not cause
any problems.
Which operating system and version are you using?
If you know a bit about programming, could you check what goes wrong in
get_nthreads_hw_avail
in src/gmxlib/gmx_detect_hardware.c ?
Add after the fo
>From the .log file:
Present hardware specification:
Vendor: GenuineIntel
Brand: Intel(R) Core(TM) i7-2600K CPU @ 3.40GHz
Family: 6 Model: 42 Stepping: 7
Features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc
pcid pclmuldq pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 sss
Hi,
This looks like our CPU detection code failed and the result is not handled
properly.
What hardware are you running on?
Could you mail the 10 lines from the md.log file following: "Detecting
CPU-specific acceleration."?
Cheers,
Berk
> Date: Tue,
LinkedIn
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--
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I'd like to add you to my professional network on LinkedIn.
- Yi
Accept invitation from Yi Gao
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Hi,
I am trying to use the Expanded Ensemble (EE) method to compute the free energy
of solvation of a small organic molecule.
Basically I am playing around but I cannot get the simulations to run.
Here are my EE and free energy settings:
%---
Hi,
I am using the latest git version of gromacs, compiled with gcc 4.6.2 and
openmpi 1.6.3.
I start the program using the usual mpirun -np 8 mdrun_mpi ...
This always leads to a warning:
Using 1 MPI process
WARNING: On node 0: oversubscribing the available 0 logical CPU cores per
node with 1 MPI
On Feb 5, 2013, at 8:22 AM, bipin singh wrote:
Hello All,
Please let me know whether is it possible to manually assign the
velocity
for each atom in the simulation instead of generating through gen_vel
option.
If the preceision of a gro-file is sufficient you can use such for
manually s
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