Use make_ndx to put all your groups in one .ndx file. It's totally
unnecessary to use multiple .ndx file in one command.
Terry
On Tue, May 28, 2013 at 10:18 AM, Kieu Thu Nguyen wrote:
> Dear users,
>
> Is there command for using many different index.ndx files in one command
>
Check this: http://manual.gromacs.org/online/editconf.html
editconf -align
On Fri, Jan 25, 2013 at 1:12 PM, 申昊 wrote:
> Dear GMX users,
>
>I have a question about aligning my molecules along specific coordinate
> axis ,such as Z-axis.
>Does anyone know the codes?
>
>
> Best regards,
>
http://www.gromacs.org/Documentation/Installation_Instructions/Cmake#double_precision_build
Terry
On Thu, Oct 18, 2012 at 3:07 PM, Albert wrote:
> hello:
>
> I found with the default parameters of cmake, we can only get the single
> precision gromacs 4.6. I am wondering how can we
The TOTAL number of cores is specified by -np option. So it's 8 in all. By
the way, you can submit the job to see how. It'd be faster than waiting on
the list.
Terry
On Thu, Oct 18, 2012 at 3:20 PM, Albert wrote:
> hello:
> I've got a qeustion the CPU for replica excha
.gromacs.org/online/gro.html
http://manual.gromacs.org/online/top.html
There are no charges in .gro files. The charges are probably discarded in
your way.
Terry
gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the arch
You should paste your topology for you metal halides so that others can
help.
On Fri, May 11, 2012 at 9:48 PM, Anik Sen wrote:
> Hi, Am Anik Sen. AM using GROMACS 3.3.2 for one of my work.
>
> I was trying to run the dynamics for some inorganic metal
> halides solvation in water. A
On Fri, May 11, 2012 at 2:18 PM, Sangita Kachhap wrote:
>
> Hello all
> I am runing Gromacs Tutorial KALP-15 in DPPC (I am using POPC)
> I am geeting error during addiotion of ions
> Fatal error:
> Your solvent group size (12548) is not a multiple of 3
> For more information and tips for troublesh
ot;
Based on the information you provided, the only thing I can say is, MAYBE
your system is "too small" to run with 256 processors.
Cheers
Terry
On Fri, Jan 6, 2012 at 3:45 PM, Albert wrote:
> thank you very much for kind reply.
>
> I change my command as following:
>
Hi,
You should start from here:
http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm
Terry
On Fri, Jan 6, 2012 at 12:49 PM, Albert wrote:
> Hello:
> I found that each time I
This is what you are looking for:
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts?highlight=scripting
Terry
On Tue, Nov 15, 2011 at 11:42 AM, Liu, Liang wrote:
> I am wondering if there is a flag to make the command select SOL
> automatically instead of pressin
You should issue a "q" command to save and quit. So "choice.txt" should look
like:
ri 1-20
...
...
ri 101-120
q
Cheers.
Terry
On Fri, Jul 22, 2011 at 1:53 PM, Chandan Choudhury wrote:
> Hi gmx-users,
>
> I was trying to feed make_ndx with the non-interactive
Hi Chuan,
Leap is a part of Ambertools which is free. See
http://ambermd.org/#AmberTools
Good luck.
Terry
2011/4/20 Liao Chuan
> HI, Itamer and Mark, thanks for your prompt replies.
>
> Pymol, Amber and Sybyl are commercial software. Any free software/scripts?
>
&
"inconsistent shifts" lines
which I ignored before.
I still don't understand why g_sas can work with the first three trjs but
the last one in the same for loop.
Terry
On Wed, Mar 30, 2011 at 5:05 PM, Mark Abraham wrote:
> On 30/03/2011 5:58 PM, Terry wrote:
>
>>
ginning ). I deleted the -q flag and run g_sas again, seg fault again.
After searching, I did this:
source /usr/local/gromacs/bin/GMXRC
Then g_sas worked fine( without the -q flag).
But I've already sourced GMXRC.bash.
Any clue?
Terry
--
gmx-users mailing listgmx-users@gromacs.org
aints ]
> ; i funct fcxfcyfcz
>11 1000 1000 1000
> #endif
>
>
> [ system ]
> ; Name
> protein
> 128-Lipid DPPC Bilayer
>
> [ molecules
d the configure log file to
see what's wrong. I suggest you go to a experienced Linux user for help if
you don't want to figure out how configure and make work.
Terry
>
>
> On Thu, Dec 23, 2010 at 10:46 PM, Mark Abraham wrote:
>
>> On 23/12/2010 9:12 PM, Sergio Manzetti
sure coupling if it's possible?
>
>
Do you mean energy minimization with pressure coupling?
Terry
>
> Sure, that's in the manual and covered in tutorials.
>
> Mark
>
>
> Is there a workaround if there is no direct way?
>
> Thanks!
>
> Ting
>
>
have caheceked gromacs website
>
> export DSSP=/path/to/dssp
>
> setenv DSSP /path/to/dssp
>
> commands are written.
> Could you write export DSSP=/path/to/dssp command according to me.
>
>
You should issue:
export DSSP=/home/m/DSSP
See, "/home/m/DSSP" is ac
gt;
>
>> 2. I want to keep going the previous completed energy minimization by
>> increasing nsteps. How can I do this?
>>
>
> increase in nsteps, and may be the tolerance too.
>
>
>>
>> Actually, you need to start from the output .gro file, and *decrease* the
r *28* atoms. Does that
number remind you anything?
Terry
On Wed, Sep 22, 2010 at 6:42 PM, Natalie Stephenson <
natalie.stephen...@postgrad.manchester.ac.uk> wrote:
> Hi everyone,
>
> I was hoping you could clear up a problem I'm having when performing energy
> mini
Hi all,
I am new to gmx. I want to use potassium ions in my system. But grompp gives
me only error. So I go through ffG53a6.atp, but find no atom type for
potassium.
Is this normal or I made some mistakes? If this is normal, how can I use
potassium ion with ffG53a6?
Thanks
Terry
--
gmx-users
Hi,
Sorry for my mistake before, column 17 should be alternative location code,
not blank.
Good luck
Terry
2009/11/21 leila karami
> Hi
>
> I used amber03 force field in gromacs to study pr-dna interaction.
> I compare my pdb file and ffamber03.rtp file.
> I should correct
Hi Leila,
I think it is a pdb format problem. According to pdb convention, column 17
should be left blank and columns 18-20 are used for residue name.
Please check your pdb format first. Good luck.
Terry
2009/11/21 leila karami
> Hi
>
> I used amber03 force field in gromacs to stu
ror is:
>
> Error 0 [file "unk.itp",line 4]
>
> Not enough parameters
>
> …..
>
> Fatal error:
>
> Bonded/nonbonded atom type '1' not found!
>
> My pro.top file:
>
>#include “ffg43a1.itp”
>
>
Did you input this line w
n 3.3 manual). Considering the units of k_c, is 500kJ/mol
way off?
--
Cheers,
Terry
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Please search the archive at http://www.gromacs.org/search before po
?
No! The ports are numbered to coincide with GROMACS releases, and minor
differences between GROMACS versions render the ports non-interchangable.
--
Cheers,
Terry
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> 22 45 1 90 10001
>
> Would someone comment on:
> - Is this is all I need to do to restrain a1-12 wrt z-axis?
> - Are the above parameters (theta/K/multiplicity) reasonable/correct?
> - with this I should expect a1 and a2 stay in xy-plane (with their z
> co
minimization, equilibration and
production?
Thanks.
--
Cheers,
Terry
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Please don&#
Hi,
I am trying to view my GROMACS ".xvg" outputs (2D plots) in windows XP
environment. Can anyone please suggest a good way to do this?
--
Cheers,
Terry
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words, in the above example replacing
start.tprwith
three.tpr will not change the outcome?
Cheers,
Terry
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