Dear, all
I just begin to work in gromacs.
I would like to run on a protein with amber99.
Is there someone here that successfully did a protein simulation in
GROMACS with implicit solvent and willing to explain the procedure and
share the parameters used (especially force field).
In mdout.mdp (gro
Hi!
Starting an implicit solvent simulation works just as starting a "normal",
explicit solvent simulation, except there is no solvent molecules.
You should use version 4.5.3 for this though (4.0.5 will not work).
Then you specify in the mdp-file implicit_solvent = GBSA and use pdb2gmx,
grompp
Thanks!
If I understand you correctly, I need to do this (?):
1.
pdb2gmx
2.
Adding ions (if I have no SOL, what is better to choose on this step?)
3.
Minimization with mdp file, that includes these lines:
implicit_solvent = GBSA
gb_algorithm = {Still,HCT,OBC}
sa_a
Thanks again!
Don't you know how to make a total charge = 0 in this case, if implicit salt
concentration is not implemented currently? Or it is not critically?
2011/3/10 Per Larsson
> Hi!
>
> Yes, except that in point 2, I'm not sure about the effects of explicit
> ions in an implicit solvent.
>
Hi!
The answer is that I do not now critical it is.
I have seen some papers that seem to hint at it not being overly critical, but,
again, life does not come at a net charge.
You'd have to see for yourself in your system, given the observables that are
important I suppose.
Possibly we can implem
Dear all,
I have a PDB file of a protein that is in dimeric form, with an INTERchain
disulphide bridge. However, in their paper the crystallographers are not
sure if this is a true dimeric form or a cyrstallographic artefact (PQS
server suggests it is a true dimeric form, but with low confidence).
Anna Marabotti wrote:
Dear all,
I have a PDB file of a protein that is in dimeric form, with an
INTERchain disulphide bridge. However, in their paper the
crystallographers are not sure if this is a true dimeric form or a
cyrstallographic artefact (PQS server suggests it is a true dimeric
fo
Dear Mark Abraham (and anyone else interested),
I have implemented your suggestion, changing in the status.mdp file to
integrator = md and adding continuation = yes (this is the new name of
the unconstrained_start parameter); however, this did not have any
effect - the energy remained as before, d
Dear Justin,
thank you very much. Yes for sure bonds do not "break" during EM (I should
have better said "disappear"), that's why it looked strange to me. In any
case, I will do the check: if this bond will fall outside specifications in
specbond.dat I will conclude that it is only a crystallograp
Anna Marabotti wrote:
Dear Justin,
thank you very much. Yes for sure bonds do not "break" during EM (I should
have better said "disappear"), that's why it looked strange to me. In any
case, I will do the check: if this bond will fall outside specifications in
specbond.dat I will conclude that
Hi!
When you are computing your zero-step energies, do you then start from the
gro-file that you got from em? If so, maybe the energies changes because
gro-files have a fixed precision format (with three decimals), while the
em-calculations are done using either full single or double precision.
Dear gromacs users,
I need to convert namd topology (.psf file) in gromacs format (.top).
Any suggestion?
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Hi,
in most cases the easiest way is to regenerate the topology in
pdb2gmx. If that is not possible for some reason, you can use a
version of psfgen we developed in our lab:
http://www.benlabs.net/psfgen+top/Overview.html
BTW: Please don't cross-post to both gmx-users and gmx-developers.
Roland
Dear all
>From Table 5.6 of Gromacs 4.5.4 manu, position restrain constants can be
interpolated in free energy calculations. However, I cannot find how to set
up this. Can somebody help?
thanks.
dawei
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On 03/08/2011 10:23 PM, Justin A. Lemkul wrote:
Steve Vivian wrote:
New to Gromacs.
Worked my way through the tutorial with relatively few issues until
the Equilibration stage. My system blows up!!
Returned to the Topology stage and rebuilt my system ensuring that I
followed the procedu
Steve Vivian wrote:
On 03/08/2011 10:23 PM, Justin A. Lemkul wrote:
Steve Vivian wrote:
New to Gromacs.
Worked my way through the tutorial with relatively few issues until
the Equilibration stage. My system blows up!!
Returned to the Topology stage and rebuilt my system ensuring that
Hi Mark,
Thanks for your feedback. The simulations are running now again.
I got one questions, I think it will be also of interest for the
others on the mailinglist.
I used "grompp" with the "-t state0.cpt" option, are the starting
velocities taken from the cpt files or are the assigned randomly
Henri Mone wrote:
Hi Mark,
Thanks for your feedback. The simulations are running now again.
I got one questions, I think it will be also of interest for the
others on the mailinglist.
I used "grompp" with the "-t state0.cpt" option, are the starting
velocities taken from the cpt files or are
Hi All,
I've been troubleshooting a problem for some time now and I wanted to report it
here and solicit some feedback before I submit a bug report to see if there's
anything else I can try.
Here's the situation: I ran some free energy calculations (thermodynamic
integration) a long time ag
Hi, all,
I was trying to reproduce the viscosity results of SPC water reported in
Berk Hess' paper (JCP, vol.116 No.1, 209-217, 2002) by using the
periodic perturbation method. After reading some old tips on the
maillist exchanged by Song, David, etc., I tried to set up the NVT
simulation jus
There have been several bug fixes related to viscosity calculations since the
release of version 4.5.3, of which at least one (on 1/10/2011) specifically
mentions zero viscosity in the .edr and .log files.
I would suggest pulling the latest release-4-5-patches from the git repository
and try
Hi,
Please don't #include "ions.itp" in your topology file if not needed.
moeed
On 10 March 2011 13:22, tao wei wrote:
> Hi
>
> I saw your post on Gromacs forum about the
>
> Fatal error:
> Atomtype CU2+ not found
>
> http://lists.gromacs.org/pipermail/gmx-users/2010-September/053804.html
>
>
Hello,
If you need to keep ions.top then see the below link:
http://lists.gromacs.org/pipermail/gmx-users/2010-September/054487.html
moeed
On 10 March 2011 14:53, tao wei wrote:
> Dear Moeed,
>
> Thanks a lot for your quick response!
> That is problem. I do need to include ions.itp.
>
> Is th
Looks what shows up when you search the GROMACS website
(http://www.gromacs.org/)
http://www.gromacs.org/Special:Search?search=qmmm&ns=main&path=
Top two links provide all the information you require.
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceu
Hi,
I) I have been trying to figure out where is the source of the following
warning message coming from:
WARNING: masses and atomic (Van der Waals) radii will be determined
based on residue and atom names. These numbers can deviate
from the correct mass and radius of the atom t
simon sham wrote:
Hi,
I) I have been trying to figure out where is the source of the following
warning message coming from:
WARNING: masses and atomic (Van der Waals) radii will be determined
based on residue and atom names. These numbers can deviate
from the correct mass a
Dear Justin,
We recently experienced a similar problem (LINCS errors, step*.pdb
files), and then GROMACS usually segfaulted. The cause was a
miscompiled copy of GROMACS. Another member of our group had compiled
GROMACS on an Intel Core2 quad (gcc -march=core2) and tried to run the
copy without m
Hi Matt,
Thanks for the reply. I can't trace the problem to a specific compiler. We
have a PowerPC cluster with two partitions - one running Mac OS X 10.3 with
gcc-3.3, the other running YellowDog Linux with gcc-4.2.2. The problem happens
on both partitions. There are no seg faults, the r
Hi Justin,
I should have specified that the segfault happened for us after we got
similar warnings and errors (DD and/or LINCS), so the segfault may
have been tangential. Given that everything about your system worked
before GROMACS 4.5, it's possible that your older compilers are
generating code
Hi Matt,
Thanks for the extensive explanation and tips. I'll work through things and
report back. It will take a while to get things going through (unless one of
the early solutions works!) since I have no admin access to install new
compilers, libraries, etc. and for some reason the only t
Hi,
I am trying to running the Gromacs application in more than 10 node beowulf
cluster if i run the gromacs application in 5 node cluster it is not
showing any error. If i increase the number of nodes it throws the
communication error in mpich and program ends abruptly. Is it possible to
run the
Hi, all-
Have you tried running
constraints = hbonds?
That might eliminate some of the constraint issues. Much less likely
for LINCS to break or have DD issues if only the hbonds are
constrained. 2 fs is not that big a deal for the heteroatom bonds.
Best,
Michael
On Thu, Mar 10, 2011 at 8:04
Michael Shirts wrote:
Hi, all-
Have you tried running
constraints = hbonds?
That might eliminate some of the constraint issues. Much less likely
for LINCS to break or have DD issues if only the hbonds are
constrained. 2 fs is not that big a deal for the heteroatom bonds.
I haven't yet,
On 11/03/11, Kannan Govindarajan wrote:
> Hi,
>
> I am trying to running the Gromacs application in more than 10 node beowulf
> cluster if i run the gromacs application in 5 node cluster it is not
>
> showing any error. If i increase the number of nodes it throws the
> communication error i
Hi All:
I am doing free energy calculation in Gromacs and want to get an error
estimate of my results. Is it possible to compute the autocorrelation time
of dVpot/dlambda in Gromacs using a certain length of trajectory such as 10
ns? Thanks a lot
Steve Zhu
Biochem@UI
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Dear Gromacs users,
I would like so simulate a protein with phosphorylated amino acids with Gromacs
4.5.3. To do so, I got the "ffG43a1p" forcefield available from the user
contributions section (subsection force fields) and adapted the parameters
given there to Gromos53a6.
The problem now
Hello,
i) I use a NPT ensemble to get the heat capacity c(p). But I always get c(V)
when I use option -vis where some properties are listed. What is the standard
way to extract the isobaric heat capacity? Which tool should I use?
ii) The thermal compressibility is never listed when I use g_ener
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