Hello!
I have a similar problem with installing gromacs on a dual core machine.
When I go through the procedure described by Matheus Fazian Ige Gondo a bit
further down installing lam/mpi then fftw and finally gromacs everything seems
to be working fine, but lam/mpi doesn't recognize the two
Jens Pohl wrote:
Hello!
I have a similar problem with installing gromacs on a dual core machine.
When I go through the procedure described by Matheus Fazian Ige Gondo a bit further down installing lam/mpi then fftw and finally gromacs everything seems to be working fine, but lam/mpi doesn't
Jens Pohl wrote:
Hello!
I have a similar problem with installing gromacs on a dual core machine.
When I go through the procedure described by Matheus Fazian Ige Gondo a bit further down installing lam/mpi then fftw and finally gromacs everything seems to be working fine, but lam/mpi doesn't
Hello!
Check out
http://wiki.gromacs.org/index.php/Errors#Stepsize_too_small.2C_or_no_change_in_energy._Converged_to_machine_precision.2C_but_not_to_the_requested_precision
Cheers
/Per
12 mar 2008 kl. 11.58 skrev s lal badshah:
Dear gromacs experts,
I have run the energy minimization of a
Dear Gromacs Users,
I simulated the preequilibrated box of DMSO that is located in the
Gromacs Force Field Distribution with the G53a6 Gromos FF parameters
(adapted from the Geerke et. al paper in J Phys Chem B, 108 (2004)).
After temperature equilibration I performed a NPT run but in
Hi,
Did you make your DMSO molecule completely rigid?
Berk.
Date: Wed, 12 Mar 2008 12:18:08 +0100
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: [gmx-users] DMSO G53a6 FF in Gromacs
Dear Gromacs Users,
I simulated the preequilibrated box of DMSO that is located in the
First thanks for the answers. I checked several sections of the
trajectory, but the deviation is always the same, even when disregarding
the first 500 ps or looking only at the last 500 ps of the trajectory
where everything is nice equilibrated. I think the error is
insignificantly small
Hi Berk,
I used weak berendsen temperature coupling with tau_t = 0.1 and a ref_t
of 298.15 K. My average temperature during the NPT run (disregarding the
first 100 ps) is ca. 298.20 K (as given by g_energy).
I had another question to you, Berk, in my last mail to the list maybe
two hours ago,
Date: Wed, 12 Mar 2008 12:31:12 +0100
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: [gmx-users] Re: DMSO G53a6 FF in Gromacs
Hi Berk,
Thanks for replying so quick. I made it rigid in that way that I used
bonded interactions also for the groups that are not directly
Dear developers,
I would again like to thank David, Xavier and Berk for their very informative
explanations on RF-excl and 1-4 interactions. I am still a bit confused, though,
with Berk's very last statement on this issue. If I quote it:
The reaction field is not applied to pair (1-4) terms.
Dear all,
I think I found the reason for the deviation after hunderds of small
runs...:-): I normally used Dispersion Correction for both the energy
and pressure because in the manual the following is noted:
...The pressure correction in contrast is very large and can not be
neglected.
Date: Wed, 12 Mar 2008 17:20:19 +0100
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Re: DMSO G53a6 FF in Gromacs
Dear all,
I think I found the reason for the deviation after hunderds of small
runs...:-): I normally used Dispersion Correction for both
Thank you very much for help me.
I have try to install gromacs 3.3.3 on rhel 4.0.
I try to configure gromacs single with the command ./configure --enable-mpi
--program-suffix=_mpi--prefix=/usr/local/gromacs332, but when I try to
install, I have this error:
usr/bin/install: cannot create
Hi,
I want to output a structure in a given time, for example , in step 1 during
minimization.
I tried the following command using dump:
trjconv -f r-l_1_oplsaa.minim_traj.trr -timestep 1 -o m.pdb -s
r-l_1_oplsaa.input.tpr -t0 0 -dump 1
But It didnot work.
Output msg:
Select a group: 2
Thanks.
The trajectory starts at 125ps ?
So step 1 == 125 ps
step 2 == 250 ps
step 3 == 375 ps
Where is 125ps from ?
But
; RUN CONTROL PARAMETERS
integrator = steep
; Start time and timestep in ps
tinit= 0
dt = 0.002
Select a group: 2
Selected 2: 'Protein-H'
trn version: GMX_trn_file (single precision)
Reading frame 0 time 125.000
'nuff said. Couldn't comment on the time between frames in your file. gmxdump
will tell you, or get it from (nstxout or nstxtcout)*dt in your mdp.
- Original
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