2014-06-27 1:54 GMT+02:00 Justin Lemkul :
> If the force field you're using uses U-B angles, you should stick to that.
> If you don't need the cross-term, just specify ub0 and kub as zero, while
> leaving sensible values for theta0 and ktheta.
Well so I did and I still get this error...
--
G
Hello!
1. It seems I have encountered a minor bug (?) in repl_ex.c for
version 4.6.x (for NPT simulations only):
Line 880 (in version 4.6.5):
fprintf(fplog, " dpV = %10.3e d = %10.3e\nb", dpV, delta + dpV);
should be:
fprintf(fplog, " dpV = %10.3e d = %10.3e\n", dpV,
On 6/26/14, 9:38 PM, 라지브간디 wrote:
Thank you for your suggestion.
Moreover, it has been used by many publication.
What i want to know is " since the charges and LJ written for charmm force
field, shall i directly use this values in gromacs -charmm27 force filed
(ffnonbonded.itp) section? o
Thank you for your suggestion.
Moreover, it has been used by many publication.
What i want to know is " since the charges and LJ written for charmm force
field, shall i directly use this values in gromacs -charmm27 force filed
(ffnonbonded.itp) section? or need any manual conversion?
Da
On 6/26/14, 4:54 PM, Tom wrote:
Justin,
I compared the peromance (the time spent for mdrun) using md.log files for
the same simulatin run on Cary Linux and any other Linux system.
I agree different hardware can have different performance.
But these tests were run on the supper computer cluste
On 6/26/14, 4:28 PM, Matthew Stancea wrote:
Hello again!
Because of the help of Dr. Lemkul and Dr. Abraham, I was able to successfully
generate a gromacs topology of a cyclotide from a pdb file!
(The command I used was "pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o
conf.gro -p topol
On 6/26/14, 3:15 PM, Dawid das wrote:
I have figured out that I don't really need those U-B parameters, so I
changed function type to 1, and deleted those two last columns of zeros.
But I still get exactly the same error.
If the force field you're using uses U-B angles, you should stick to t
Just a follow-up, since the -dump option is working for you. I have also found
that -b 100 -e 100 sometimes doesn't work even where there is clearly a frame
at 100 ps. I presume that this happens when there is a bit of a rounding issue
in the simulation trajectory and the time is actually stored
Justin,
I compared the peromance (the time spent for mdrun) using md.log files for
the same simulatin run on Cary Linux and any other Linux system.
I agree different hardware can have different performance.
But these tests were run on the supper computer clusters with very good
reputations of per
Hi Chris,
It turns out that was a typo on my part, the error occurs when both -b and
-e values are set to a time that does exist in the trajectory file. -dump
seems to be working great, and thanks for the tip on including -b as well
to speed up trjconv!
Best Wishes,
Nathan
On Thu, Jun 26, 2014
Hello again!
Because of the help of Dr. Lemkul and Dr. Abraham, I was able to successfully
generate a gromacs topology of a cyclotide from a pdb file!
(The command I used was "pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o
conf.gro -p topol.top -i posre.itp -inter -ter".)
In the generat
I have figured out that I don't really need those U-B parameters, so I
changed function type to 1, and deleted those two last columns of zeros.
But I still get exactly the same error.
2014-06-26 21:05 GMT+02:00 Dawid das :
> I have just checked with original ffbonded.itp and the onyl difference
I have just checked with original ffbonded.itp and the onyl difference is
that I added new atomtypes.
2014-06-26 20:58 GMT+02:00 Dawid das :
> Thank you so much, but I run into another trouble:
>
> Generated 29890 of the 29890 non-bonded parameter combinations
> Generating 1-4 interactions: fudg
Thank you so much, but I run into another trouble:
Generated 29890 of the 29890 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 26783 of the 29890 1-4 parameter combinations
---
Program grompp, VERSION 4.5.5
So
Thanks, Justin.
I tried the minimization with just a lone cholesterol molecule, and there were
no LINCS warnings. Additionally, I tried a production run on the full system,
and it didn't seem to encounter any further issues. I suspect that you are
right in suggesting that the initial configu
On 6/26/14, 1:47 PM, Dawid das wrote:
Dear Gromacs experts,
I have succesfuly put new atom types into force field expression.
I have managed to run pdb2gms, editconf and genbox.
But when I try
grompp -f minimize.mdp -c mCherry7-solv.gro -p mCherry7.top -o minimize.tpr
then I get an error sayi
Dear Gromacs experts,
I have succesfuly put new atom types into force field expression.
I have managed to run pdb2gms, editconf and genbox.
But when I try
grompp -f minimize.mdp -c mCherry7-solv.gro -p mCherry7.top -o minimize.tpr
then I get an error saying that one od my newly inctroduced atoms
You listed:
echo 0|trjconv_mpi -f stn_wt_a_fit_1.xtc -s stn_wt_a_1.tpr -b 20002 -e
2 -o g96/stn_wt_a_1_0.g96 -novel
And your -b value is less than your -e value, so you should not get any output,
which is what happens.
Try using -dump to extract a single frame. If you want, you can also sup
Dear Users,
the option -equiv in the g_rmsdist tool is completely ignored. The
output in the noe.dat is same with and without the -equiv input.
For example i specify in the equiv.dat:
2 PRO HG1 2 PRO HG2
and get in the noe.dat in one line:
8 15 HG1 PRO 2 13 25 H LYS 3 0.506 0.499 6
Like I suggested last time, find somewhere mdrun does work, e.g. 1 node.
When you have a complex problem, simplify it and see what you learn ;-) If
mdrun explodes on 1 node, try your .tpr on a local machine, to see whether
it's the mdrun install, or MPI system that could be at fault, or maybe it's
On 6/26/14, 10:25 AM, Nathan Scott wrote:
Justin,
I actually must have mistyped that, the command below also fails with the
same error.
echo 0|trjconv_mpi -f stn_wt_a_fit_1.xtc -s stn_wt_a_1.tpr -b 20002 -e
20002 -o g96/stn_wt_a_1_0.g96 -novel
I will explore -dump though, thanks for the sug
Justin,
I actually must have mistyped that, the command below also fails with the
same error.
echo 0|trjconv_mpi -f stn_wt_a_fit_1.xtc -s stn_wt_a_1.tpr -b 20002 -e
20002 -o g96/stn_wt_a_1_0.g96 -novel
I will explore -dump though, thanks for the suggestion!
Best Wishes,
Nathan
On Thu, Jun 26
On 6/26/14, 10:02 AM, Nathan Scott wrote:
Hi all,
I am trying to use trjconv to extract .g96 files iteratively, then use my
own software for analysis, then delete the .g96 file, but I am running into
perplexing behavior. I did a bit of searching in the list archive but can
find no mention of t
On 6/26/14, 8:28 AM, xiao wrote:
Dear gromacs users,
I want to change the dihedral angle during simulation. For example, i want to
change the dihedral from 30 to 90 gradually during the simulation. Can i use
the pull code? If not, how can i do it in the simulation.
See manual section 6.5
Hi all,
I am trying to use trjconv to extract .g96 files iteratively, then use my
own software for analysis, then delete the .g96 file, but I am running into
perplexing behavior. I did a bit of searching in the list archive but can
find no mention of this, so it could well be I am just doing somet
Hi all,
I am trying to use trjconv to extract .g96 files iteratively, then use my
own software for analysis, then delete the .g96 file, but I am running into
perplexing behavior. I did a bit of searching in the list archive but can
find no mention of this, so it could well be I am just doing somet
Thank you Justin!
Now I am going to try
Ivan
On 06/26/2014 01:49 PM, Justin Lemkul wrote:
On 6/26/14, 6:21 AM, Ivan Gladich wrote:
Dear all,
I am trying to build a cyclic peptide of 12 aminoacids using
pdb2gmx.
Searching on the web I found that is not very straightforward without
edit
Dear gromacs users,
I want to change the dihedral angle during simulation. For example, i want to
change the dihedral from 30 to 90 gradually during the simulation. Can i use
the pull code? If not, how can i do it in the simulation.
Best regards
Fugui
--
Gromacs Users mailing list
* Pleas
Thanks for the insights.
So, now using the .tpr file generated with grompp whose version matches the
mdrun.
files are generated again but after time step 0 and time 0 nothing gets
written and the jobs reaches an error state and stops.
in the error file,
mpirun noticed that process rank 41 with
On 6/26/14, 4:50 AM, #ZHANG HAIPING# wrote:
Dear gromacs user:
I recently viewed a paper which says the number of exchange attempts should be
chosen to significantly exceed the transit number for for the replica-exchange
scheme. But I don't know where to set the number of exchange attempts i
On 6/26/14, 6:21 AM, Ivan Gladich wrote:
Dear all,
I am trying to build a cyclic peptide of 12 aminoacids using pdb2gmx.
Searching on the web I found that is not very straightforward without editing
the topology and the .gro file
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users
In my opinion, it is an acceptable solution to take these parameters as is.
Especially, if you write some wise words about philosophy of FF
compatibility/trasferability and pairwise interactions for your
methodology section.
Dr. Vitaly V. Chaban
On Wed, Jun 25, 2014 at 8:02 AM, Mark Abraham w
Dear all,
I am trying to build a cyclic peptide of 12 aminoacids using pdb2gmx.
Searching on the web I found that is not very straightforward without
editing the topology and the .gro file
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-September/074609.html
The problem is
I have solved this problem, by letting -vdwd option of genbox take its
default value rather than my first value of 0.55.
Thanks
Chetan
On Wed, Jun 25, 2014 at 7:52 PM, Chetan Mahajan
wrote:
> Just to be complete: I am using following command to populate system with
> SPC water using genbox:
>
>
Dear gromacs user:
I recently viewed a paper which says the number of exchange attempts should be
chosen to significantly exceed the transit number for for the replica-exchange
scheme. But I don't know where to set the number of exchange attempts in
replica exchange simulation. Can anyone help,
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