[gmx-users] Re: amber force field in Gromacs
Hi Alan,
Thank you for all your efforts. This is getting strange, I tried
following your procedure below but is still does not work for me:
step 3500, will finish Fri Dec 4 09:56:51 2009Warning: 1-4 interaction
between 6 and 10 at distance 1.454 which is larger than the 1-4 table
size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
kind regards,
Servaas
Message: 1
Date: Thu, 3 Dec 2009 11:23:14 +
From: Alan alanwil...@gmail.com
Subject: [gmx-users] Re: amber force field in Gromacs
To: gmx-users@gromacs.org
Message-ID:
cf58c8d00912030323v97c0556oa6aa1942c4625...@mail.gmail.com
Content-Type: text/plain; charset=utf-8
Dear Servaas,
Tested again in 'vacuum' and I saw no problems. Here goes what I did:
#--
cat EOF | leap.in
verbosity 1
source leaprc.ff99SB
ad = sequence { DA5 DA DA3 }
saveamberparm ad da_amber.top da_amber.crd
savepdb ad DA.pdb
quit
EOF
tleap -f leap.in | leap.out
acpypi -x da_amber.crd -p da_amber.top -d # acpypi generates em.mdp and
md.mdp
cat EOF | md.mdp
cpp = /usr/bin/cpp
define = ;-DFLEXIBLE
integrator = md
nsteps = 25
constraints = none
emtol= 1000.0
emstep = 0.01
comm_mode= angular
ns_type = simple
nstlist = 0
rlist= 0
rcoulomb = 0
rvdw = 0
Tcoupl = no
Pcoupl = no
gen_vel = no
nstxout = 100
pbc = no
EOF
editconf -bt cubic -d 1.0 -f da_amber_GMX.gro -o da_amber_GMX.gro
#Single precision
grompp -f em.mdp -c da_amber_GMX.gro -p da_amber_GMX.top -o em.tpr
mdrun -v -deffnm em
grompp -f md.mdp -c em.gro -p da_amber_GMX.top -o md.tpr
mdrun -v -deffnm md
vmd md.gro md.trr
#--
As you may suspect from the beginning it may be something in your mdp file.
Case the example above works, I would suggest you to try the mdp for solvent
box I sent before in a long simulation.
Good luck.
Regards,
Alan
On Wed, Dec 2, 2009 at 11:10, Alan alanwil...@gmail.com wrote:
Dear Servaas,
In tleap did you really did:
TLEAP
tleap -f leaprc.ff99SB
ad = sequence { DA5 DA DA3 }
saveamberparm da da_amber.top da_amber.crd
If so, it's wrong, it should be:
saveamberparm ad da_amber.top da_amber.crd
^^^
and not 'da'
Besides, I tried to reproduce what you did using what I think would be
fine and... everything went fine! Energies after minimisation in
single and double were almost identical and trajectories diverted
normally.
Please check what I did.
# begin commands
cat EOF | em.mdp
define = -DFLEXIBLE
integrator = cg ; steep
nsteps = 200
constraints = none
emtol= 1000.0
nstcgsteep = 10 ; do a steep every 10 steps of cg
emstep = 0.01 ; used with steep
nstcomm = 1
coulombtype = PME
ns_type = grid
rlist= 1.0
rcoulomb = 1.0
rvdw = 1.4
Tcoupl = no
Pcoupl = no
gen_vel = no
nstxout = 0 ; write coords every # step
optimize_fft = yes
EOF
cat EOF | md.mdp
integrator = md
nsteps = 1000
dt = 0.002
constraints = all-bonds
nstcomm = 1
ns_type = grid
rlist= 1.2
rcoulomb = 1.1
rvdw = 1.0
vdwtype = shift
rvdw-switch = 0.9
coulombtype = PME-Switch
Tcoupl = v-rescale
tau_t= 0.1 0.1
tc-grps = protein non-protein
ref_t= 300 300
Pcoupl = parrinello-rahman
Pcoupltype = isotropic
tau_p= 0.5
compressibility = 4.5e-5
ref_p= 1.0
gen_vel = yes
nstxout = 2 ; write coords every # step
lincs-iter = 2
DispCorr = EnerPres
optimize_fft = yes
EOF
cat EOF | leap.in
verbosity 1
source leaprc.ff99SB
ad = sequence { DA5 DA DA3 }
solvatebox ad TIP3PBOX 10.0
addions ad Na+ 5
addions ad Cl- 3
saveamberparm ad da_amber.top da_amber.crd
savepdb ad DA.pdb
quit
EOF
tleap -f leap.in | leap.out
acpypi -x
Re: [gmx-users] Re: 1-4 interaction energies in g_energy
Vitaly V. Chaban wrote: Hi, Please suggest why is the reason that 1-4 term is not displayed (to be selected for calculation) in the g_energy utility? I have two kinds of objects (with 25 and 5 atoms) in my system - with nexcl equal to 3 and 2. I guess the 1-4 term may not be displayed if there is no 1-4 interactions but in this system they are evidently present. What the problem can be here? Hard to say - we can't see your topologies or even know what your objects are. You may have some manual exclusions or some such. What do you mean saying manual exclusions? I have no energy exclusions defined in grompp.mdp. Is there any place to make them? See second para of 5.4 Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] What is the exact difference in the g_energy output between LJ(1-4) LJ(SR) and LJ(LR)?
Justin A. Lemkul ha scritto: As per the title. I need to understand what is the difference to help myself debug my inane efforts at CG parametrization. LJ(1-4) I think is clear (non bonded, non-coulombic interactions between 1-4 pairs described in the topology), but about the rest? See manual 4.6.3 Seen it, still don't get it :) A good reason to search the mailing list... http://lists.gromacs.org/pipermail/gmx-users/2007-December/031264.html Uh, thanks! I always google the ML before asking, but my googling skills are evidently not as good as I thought. Thanks! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] RF and TI
Dear gmx users, I calculated the hydration free energy of benzene molecule two times. First time I used a decoupling method implemented in GROMACS. Second time I performed thermodynamical integration between different topologies of the benzene molecule: non-interacting with media and normal one. All intramolecular interactions were turned off. The results were different: decoupling method gave energies about 2.8 kcal/mol higher. I investigated the problem and found that the difference of the dH/dl values was due to the Reaction-field term. When I switched electrostatic to the simple cut-off scheme, decoupling method gave almost the same result, while for dual topology method the result increased on 2-3 kcal/mol. Is the RF method consistent with free energy calculations? Can it be treated within the frames of decoupling scheme? Thanks, Alexey -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] RF and TI
Hi, Yes, RF in the couple scheme is correct. The manual calculation you did is incorrect. In the decoupled state the intra-molecular interactions of the decoupled molecule should not be RF, but plain Coulomb. The couple option does this correctly. Berk Date: Fri, 4 Dec 2009 15:52:58 +0300 From: ale.odino...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] RF and TI Dear gmx users, I calculated the hydration free energy of benzene molecule two times. First time I used a decoupling method implemented in GROMACS. Second time I performed thermodynamical integration between different topologies of the benzene molecule: non-interacting with media and normal one. All intramolecular interactions were turned off. The results were different: decoupling method gave energies about 2.8 kcal/mol higher. I investigated the problem and found that the difference of the dH/dl values was due to the Reaction-field term. When I switched electrostatic to the simple cut-off scheme, decoupling method gave almost the same result, while for dual topology method the result increased on 2-3 kcal/mol. Is the RF method consistent with free energy calculations? Can it be treated within the frames of decoupling scheme? Thanks, Alexey -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ New Windows 7: Find the right PC for you. Learn more. http://windows.microsoft.com/shop-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] xmgrace
While running MD simulation I have number of queries mentioned below: 1. When executing xmgrace command it returns the bash command not found, then how to install GRACE package on windows? 2. When defining the box dimention then how do I know about the distance of protein (207 residues) from the box wall should be greater than half of the Cut-Off (1.4nm)? 3. In fullmd_sol.mdp file how to find the time step value because I don't have confirmation about that. 4. When using grommp command to generate fullmd.tpr file, it will shows 3 notes (a.) The Berendsen thermostat does not generate the correct K.E distribution, and suggesting to use v- rescale thermostat (b.) Why the system has non-zero total charge : -2.01e+00 (c.) [file fullmd_sol.mdp, line unknow]: you are using a plain coulomb cut-off, which might produce artifacts. You might want to consider using PME electostatics. 5. How to save screen of cygwin (general question) Please solve these problems if you can I am thankful to you. -- Pawan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re:Re: helix tilt
Stefan Hoorman wrote: How can I calculate the angle between a helix inserted in a membrane and the axis perpendicular to the surface of the membrane. I have tried using g_helixorient, but the graphs all come as a straight line in zero. See -z in g_sgangle -h Mark Thank you for the tip, but again I faced a problem. I could only analyse using g_sgangle with an index group containing 3 atoms. Then the problem is, since my helix not only tilts, but also it bends a little back and forth, the angle between it and the z axis will vary greatly depending on which three atoms I choose. I imagined that by choosing three alpha carbon atoms every four residues would give me a good outcome, but it turns out that the angle changes a lot, and I am guessing it is because of this bending movement. When I say changes a lot I mean; it starts at 0º and gets up to 50º, which i imagine to be a little bit too much. Would there be a better way to calculate this? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] dihedral restraints in gromacs 4.0.5
Steven Ari Beasley wrote: has anyone successfully incorporated dihedral angle restraints in gromacs 4.0.5 protein simulation. i can only find instructions for gromacs 3.3.1, nothing in the manual. Do these instructions not work? http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints i don't know if the format is the same or whether it requires diffent .mdp flags, but so far i have not been able to successfully run a I don't believe there have been any changes as far as .mdp keywords (dihre_tau might be ignored, but I can't remember at the moment). If you post what you're trying and any errors that you receive or evidence that the restraints are not working, that would be useful in providing assistance. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] amber force field in Gromacs
This kind of problems can occur if you were restraining atom positions and using
pressure coupling.
Best regards
Lucio.
Lucio Ricardo Montero Valenzuela
PhD Student
Laboratorio del Dr. Federico Sánchez
Ext. 27666
Departamento de Biología Molecular de Plantas
Instituto de Biotecnología, UNAM
Cuernavaca, Morelos, 62210
Mensaje citado por servaas servaas.michielss...@student.kuleuven.be:
servaas skrev:
Message: 4
Date: Tue, 1 Dec 2009 13:56:21 +
From: Alan alanwil...@gmail.com
Subject: [gmx-users] Re: amber force field in Gromacs
To: gmx-users@gromacs.org
Message-ID:
cf58c8d00912010556k5f2c918eqb2e1608c5c4cf...@mail.gmail.com
Content-Type: text/plain; charset=UTF-8
Dear Servaas,
I've been following your thread. I am the developer of acpypi and
thanks for giving a try.
So, as you may already know, you are trying acpypi as amb2gmx.pl so
far, but you also seemed to have read acpypi wikis and realise that
acpypi can help you to generate the whole topology for a ligand.
However, AFAIU you have only regular NA and not modified ones neither
ligands, right? But then why are you using RED?
I generated own parameters, had an error tried to find out the problem,
eventually I tried with natural NA and got exactly the same problem.
(The modified molecule was very similar to natural nucleic acids)
I understand your approach about using tleap to create your whole
system and then convert it to GMX. It should work at first but it is
clearly not as you reported.
So, here goes some of my recommendations:
1) GMX is vacuum is unrealistic and prone for errors. There's no GB
implementation as far as I know.
True, but as all ready stated, in AMBER I can simulate this compound
without any problems in vacuum.
I also ran the simulation in gromacs with a solvent box and counter ions,
same problem.
So it is not a vacuum artefact.
2) Have you try to use pdb2gmx to generate your files from your pdb
directly to GMX?
Not yet, I could ideed try this for the natural sequence, but the
problem persists then for my modified molecule...
3) When you say that gmx double precision works, is your system in
vacuum or with solvent?
Double precisions works both in solvent and in vacuum, single precision
never...
4) if using tleap, create your system with solvent and ions and then
use acpypi to convert to gmx.
What problems do you expect from creating it in amber without solvent
box and creating the box in gromacs? I applied this procedure before
with success. (although this was with amb2gmx.pl, which I also tried
here)
The use of amb2gmx or acpypi is to give you a system to be run
immediately in gromacs doing just a grompp and mdrun. Using editconf
will change the parameters of your box and it may have serious
implications besides that in amber we don't have dodecahedron, so if
doing what you're doing then you're not replicating the conditions you
have in amber with those in gmx (although it puzzles me that gmx
double works, with the commands you gave in gmx?).
Do you realy expect serious problems from this? Creating a molecule in
vacuum and adding the box in GROMACS looks perfectly ok to me. Adding a
box only adds a line in the .gro file about the box parameters, I do not
see how this could influence anything else...
Well, it could. Are you using pbc or not? If you are then the rhombic
dodecahedron will indeed cause the periodic copies to be more closely
packed than for other boxes. I couldn't see any mentionong of pbc in
your mdp file.
/Erik
Yes of course the box could make a difference, but what I meant was does
it make a difference if I create it in GROMACS or AMBER. I also tried
running without PBC and with larger boxes, without luck...
I would ask you to give more details and even a detailed step by step
of commands of what you're doing including tleap.
Ok, to keep things simple for the case of the natural NA:
TLEAP
tleap -f leaprc.ff99SB
ad = sequence { DA5 DA DA3 }
saveamberparm da da_amber.top da_amber.crd
ACPYPI or AMB2GMX
python acpypi.py -x ad_amber.crd -p ad_amber.top -o gmx -b ad_gro
or with amb2gmx.pl
./amb2gmx.pl --prmtop ad_amber.top --crd ad_amber.crd --outname ad_gro
GROMACS
editconf -bt dodecahedron -d 1.0 -f ad_amber.gro -o ad_box.gro
I run a minimization:
grompp -f md.mdp -c ad_box.gro -p ad_gro.top -o em.tpr
mdrun -deffnm em
(Also tried putting a position restraint step in between, did not
resolve the problem)
grompp -f md.mdp -c em.gro -p ad_gro.top -o md.tpr
mdrun -deffnm md
Regards,
Alan
On Tue, Dec 1, 2009 at 11:00, gmx-users-requ...@gromacs.org wrote:
Thanks for your suggestion, I tried without success and I also tried
shake. But this is also rather fighting the
Re: [gmx-users] gen_vel
leila karami wrote: Hi in which case in mdp file, gen_vel should be yes or no? ... when you want to generate velocities or not. See manual section 3.4, particularly 3.4.1 Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
