On 11/8/14 6:53 PM, Thomas Lipscomb wrote:
Dear gmx-users,
I am still following this tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
But I got an error at this step:
"Note how many lipids were deleted and update the [ molecule
This usually means that your system is not well equilibrated.
Dr. Vitaly V. Chaban
Виталий Витальевич ЧАБАН
On Wed, Oct 15, 2014 at 6:13 AM, Padmani Sandhu
wrote:
> Hello,
>
>
> I am doing Molecular-Dynamic simulation of Protein-Ligand complex embedded
> in POPC lipid membrane. After energy
Dear Ainun.
It looks like your system is exploding. Check the input coordinates.
Cheers
Cesar
El 03/10/2014 01:10, "AINUN NIZAR M" <0810710...@mail.ub.ac.id> escribió:
> Dear users,
>
> I conduct folding simulation, this is my trial project before I conduct my
> own one. I simulate small protein,
Hi,
Average structures are typically unphysical and rarely meaningful. Consider for
instance the average structure of a spinning methyl group. Representative
structures can be produced by clustering the frames in a trajectory and
selecting the cluster centroids. See g_cluster.
Kind regards,
Er
On 9/12/14 8:19 AM, Namita Singh wrote:
Yes .xvg output file got generated without errors. Kindly see to it if the
command mentioned in my previous mail is correct for getting the
residue-residue contact of protein complexes. Also as i mentioned that why
am i not getting the log file generated
Yes .xvg output file got generated without errors. Kindly see to it if the
command mentioned in my previous mail is correct for getting the
residue-residue contact of protein complexes. Also as i mentioned that why
am i not getting the log file generated even after giving the -g hbond.log?
On Fri,
On 9/12/14 6:11 AM, Namita Singh wrote:
i nwant to generate a log file for residue residue contact of a
protein-protein complex.I am using
g_hbond -s a.tpr -f c.xtc -r 0.55 -num hbond.xvg -g hbond.log -n
atom_index.ndx -contact
bt i am not getting any log file.
Do you get the other output
something wrong with the input atom index.
Thanks and Regards,
Bipin Singh
On Fri, Sep 12, 2014 at 3:44 PM, Namita Singh
wrote:
> i want to generate a log file for residue residue contact of a
> protein-protein complex.I am using
>
> g_hbond -s a.tpr -f c.xtc -r 0.55
On 9/8/14 5:33 AM, Somayeh Alimohammadi wrote:
Dear gmx users
I am performing a simulation by gromacs. for building the ligand itp file
by Prodrg, I get an error thet boron atom is not supported by this program.
Do you have any propose for solute this problem?
Choose a force field and paramet
thank you very much sir.
regards
Suriyanarayanan
On Sat, Aug 23, 2014 at 12:06 AM, Tsjerk Wassenaar
wrote:
> Hi Suriyanarayanan,
>
> You can check out the WeNMR Gromacs portal.
>
> Hope it helps,
>
> Tsjerk
> On Aug 22, 2014 10:29 AM, "Balasubramanian Suriyanarayanan" <
> bsns...@gmail.com> wr
Hi Suriyanarayanan,
You can check out the WeNMR Gromacs portal.
Hope it helps,
Tsjerk
On Aug 22, 2014 10:29 AM, "Balasubramanian Suriyanarayanan" <
bsns...@gmail.com> wrote:
> Dear Users,
>
> generally for running a 10 ns simulation is there any online server
> facility available. This will be
On 8/5/14, 9:27 AM, Balasubramanian Suriyanarayanan wrote:
Dear All,
How can we decode the md.xtc or md.tpr files. Can it be opened in word
file.
No, these are absolutely not the kind of files that you open in word processing
software.
I don't know what you mean by "decode," but you sh
On 7/14/14, 6:17 AM, Yana Tsoneva wrote:
Dear colleagues,
Firstly, I want to thank Justin Lemkul for helping me on the topic
"polarizable water and non-polarizable alkanes". Now I have to
simulate systems that consist of polarizable water and polarizable alkanes.
The chosen force field is CH
On 6/18/14, 11:43 AM, fatemeh ramezani wrote:
Dear Users
I run this command:
nohup mpirun -np 8 mdrun_mpi -s x.tpr -o x.trr -c x.pdb -g x.log -e x.edr &
Despite the use of nohup and &, mdrun will stop after closing the putty window.
Can anyone help me to solve this problem?
Google kn
Please keep the discussion on the gmx-users list.
On 6/18/14, 9:10 AM, Amninder wrote:
My mistake for subtraction but still too far from expt Value. I am using OPLS
force field and parameters from virtual chemistry.org and used conditions
corresponding to their paper.
Post your .mdp files
On 6/18/14, 1:04 AM, AMNINDER SINGH wrote:
Dear
People,
I am trying to calculate enthalpy of vaporization
of methanol.
Using energy
–nmol on equilibrated methanol, E pot comes -5.005 KJ/mol.
Then for EPot
(gas) I got 14.405 KJ/mol.
Using DHvap
= Epot(gas) - Epot (liquid)+RT.
My value
comes
i've recieved your email concernig "energy minimisation step in protein
lipid simulation" already 3 times ..
maybe you've deactivated the delivery of mails? if so, do the following:
go to https://mailman-1.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
and log in where it says "To unsubscri
then, i don't know what to do. may be your email provider sorts them out
or something.
anyway, did you get justin's answer he sent recently? see below ..
vedat
On 6/12/14, 4:54 AM, Balasubramanian Suriyanarayanan wrote:
> Dear friends, In protein lipid simulation , when I do energy minimisatio
i've recieved your email concernig "energy minimisation step in protein
lipid simulation" already 3 times ..
maybe you've deactivated the delivery of mails? if so, do the following:
go to https://mailman-1.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
and log in where it says "To unsubscri
On 6/12/14, 5:31 AM, Balasubramanian Suriyanarayanan wrote:
Why is my questions not appearing in the forum.
Do I not follow the rules.'
Please clarify.
Your messages are being posted just fine. Please stop spamming the list.
-Justin
--
==
thanks venkat.
Done
On Tue, Jun 10, 2014 at 11:19 AM, Venkat Reddy wrote:
> Hi,
> Did you modify your forcefield such a way that it applicable for lipid
> atoms also???
> If not, follow Justin's tutorial
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_prote
Hi,
Did you modify your forcefield such a way that it applicable for lipid
atoms also???
If not, follow Justin's tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html
On Tue, Jun 10, 2014 at 10:31 AM, Balasubramanian Suriyanarayanan <
bs
On 6/8/14, 2:50 AM, #ZHANG HAIPING# wrote:
Dear gromacs user:
In the online manul it says "the frequency for writing dH/dlambda and possibly Delta H to
dhdl.xvg, 0 means no ouput, should be a multiple of nstcalcenergy". But in the tutorial of
free energy circulation of methane it use "nstdh
On 6/2/14, 5:59 AM, Balasubramanian Suriyanarayanan wrote:
Dear users,
Where can we get "gromos43a1.ff" from gromacs directory> please help me.
It's present by default in $GMXLIB.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein
On 5/31/14, 2:12 AM, elham tazikeh wrote:
Dear Users
I simulated Zinc ion on human growth hormone protein by Gromacs 4.6
and encountered with this message:
there are not molculetype for Zn
this sentence means I can not simulate this system on Gromacs 4.6 and have
to install version 4.5 on my
U can do in Gromacs 4.6.
Check the alignment of Zn in your pdb file, I hope a gap (space) is
inserted before the Zn.
Good Luck.
*Cheers*
Khuraijam
On Sat, May 31, 2014 at 11:42 AM, elham tazikeh
wrote:
> Dear Users
> I simulated Zinc ion on human growth hormone protein by Gromacs 4.6
> and e
I have an interesting question reguarding NH2 attached to cyclic rings in topology files. I have seen them represented in a somewhat SP3 state, where the hydrogens are held as if there were almost 3, rather than two. I have also seen them artificially flatened with an improper dihedral, which
You should provide with more information. The error message clearly states
that there are multiple definitions for the moleculetype CU1. You should
check carefully for redundancies in the top file
On Wed, May 21, 2014 at 2:57 AM, Meenakshi Rajput
wrote:
> dear gromacs users
> I tried to add ions
http://www.gromacs.org/Support
You're emailing a list of Gromacs users and developers; compose your question as
you would any other email.
-Justin
On 4/26/14, 10:17 PM, Swetha Srinivasan wrote:
Hi,
I don't know how to post my queries.Could you help me with that.
Thanks,
Swetha
__
Hi,
I don't know how to post my queries.Could you help me with that.
Thanks,
Swetha
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Swetha
Srinivasan
Sent: Saturday, April 26, 2014 10:14 PM
To: gromacs.org_gmx-users@maillist.sys.k
this is the problem of software installation.
Reinstall software along with necessary modules.
On Mon, Apr 7, 2014 at 12:49 PM, Meenakshi Rajput
wrote:
> I tried to do perform mdrun on myo.pdb by using command "g_mdrun -v -s
> m.tpr -o minim_traj.trr -c myo.gro -e minim_ener.edr". But I got the
Hi,
That should never happen - mdrun has asked your hardware what it is, and
got told there were no CPUs at all. Can you tell us some more about your
hardware and OS, please?
Mark
On Mon, Apr 7, 2014 at 9:19 AM, Meenakshi Rajput wrote:
> I tried to do perform mdrun on myo.pdb by using command
On 3/6/14, 1:04 AM, Prajisha Sujaya wrote:
i am gettng error while doing simulation of Trna molecule i have used
gromacs and force field CHARMM27 all-atom force field (with CMAP) - version
2.0
"Residue 'ADE' not found in residue topology database". How to solve this
error
http://www.gromacs
On 2/28/14, 6:36 AM, abhijit Kayal wrote:
Thanks Justin for the help. But if I want to look the dipole auto
correlation or hydrogen bond dynamics ... is that possible?
Each frame is just a time point in the trajectory. Concatenate the individual
output and you get a time series.
-Justin
Thanks Justin for the help. But if I want to look the dipole auto
correlation or hydrogen bond dynamics ... is that possible?
On Fri, Feb 28, 2014 at 4:38 PM, Justin Lemkul wrote:
>
>
> On 2/28/14, 5:38 AM, abhijit Kayal wrote:
>
>> Dear Gromacs users,
>>
>> My system contained CNT+ wat
On 2/28/14, 5:38 AM, abhijit Kayal wrote:
Dear Gromacs users,
My system contained CNT+ water. I have created a dynamically
index.ndx file
which contain the number of water molecules in each frame inside cnt.
Now I want to study the dipole orientation of these water molecules. But I
can
Hi Justin.
I hope you have a nice day
I would like to simulate a peptide on the membrane .In tutorial gromacs that
simulate peptide
KALP_15 in membrane DPPC ,you use inflate and shrink step.Do I need to do this
step for my system?
May you can help me؟ Thanks
On Wednesday, February 12, 2014
On Tue, Nov 26, 2013 at 4:09 AM, Mahboobeh Eslami <
mahboobeh.esl...@yahoo.com> wrote:
> hi Dear Gmx Users
> i want to study the changing of velocity in production stage, do i set
> gen_vel= yes, gen_temp = 300 and gen_seed = -1 in all mdp file for
> Equilibration and production or only in
Do a test run. mdrun -nsteps can be useful there.
On Nov 26, 2013 9:45 AM, "Mahboobeh Eslami"
wrote:
> Hi all my friends
> I need to check the speed of the production stage. What should I do.
> Thank you very much
> With respect
> --
> Gromacs Users mailing list
>
> * Please search the archive at
On 11/19/13 11:31 AM, Mohsen Ramezanpour wrote:
Hi
I think you should use the correct atomtype, accoding to this FF
atomtypes, for your atom which you have introduced as HH.
Correct. More explicitly, the trick to dealing with OPLS-AA is that its
nonbonded types (opls_*) have bonded equival
Hi
I think you should use the correct atomtype, accoding to this FF
atomtypes, for your atom which you have introduced as HH.
Best
Mohsen
On Tue, Nov 19, 2013 at 7:48 PM, fatemeh ramezani wrote:
> HI DEAR USERS
> I want to simulate collagen by OPLSAA. I added hydroxyprolin parameters as
> foll
On Mon, Nov 18, 2013 at 2:28 PM, Shima Arasteh
wrote:
> Dear gmx users,
>
>
> My simulated system contains is composed of lipid, protein and water
> molecules.
> The NPT and NVT steps were done with position restraints on protein atoms.
> Then I removed the position restraints by line ";define =
??
Surya Prakash Tiwari
On Thu, Nov 14, 2013 at 7:12 AM, Raj K wrote:
> --
> Rajesh Kumar Kesharwani C/O Prof Krishna misra
>
> M.Tech (Bioinformatics)
> Indian Institute of Information Technology-Allahabad
> Contact: +919335323082
> --
> gromacs.org_gmx-users mailing list
> gromacs.org_gmx-us
201 - 243 of 243 matches
Mail list logo
