OZGE ENGIN wrote:
Thank you for your suggestion, but I have already tried it.
If your system is periodic in (at least) the x direction, then your
peptide hasn't moved out of the box. Play with the trjconv options until
you find something that works.
Mark
raghava alapati wrote:
hi..
General i use " tpbconv " for continuing a simulation in a
single node. Can i use the same command for continuing a simulation in
parallel if so, how do i encounter the no. of processors to be used in
parallel.
No. tpbconv writes a continuation, which
Justin A. Lemkul wrote:
Try using 'tinit' instead of 't_init'
... and Sarbani should be checking his warnings from grompp, which would
have been issued for the misspelled version.
See http://wiki.gromacs.org/index.php/Doing_Restarts#Using_grompp for
general advice here.
Mark
_
hi..
General i use " tpbconv " for continuing a simulation in a single
node. Can i use the same command for continuing a simulation in parallel if
so, how do i encounter the no. of processors to be used in parallel.
--
raghava alapati
804-677-5494
__
Hi,
> i am extremely sorry here.. i am plotting dg/dl vs lambda of reverse
> transformation onto that of forward with both axes reversed. so i
> should expect overlap. this is consistent with whatever you are saying. i
> am sorry for negligence and confusion.
And taking the negative?
> >> but wh
On Mon, 5 Nov 2007, David Mobley wrote:
Hi,
it is fairly straight FORWARD.. forward is from state A to state B, and
reverse is from state B to state A. Say for example, forward
transformation is going from ethane to methane. in this step, i define
three of the terminal hydrogen on say C2, with
Hi,
> it is fairly straight FORWARD.. forward is from state A to state B, and
> reverse is from state B to state A. Say for example, forward
> transformation is going from ethane to methane. in this step, i define
> three of the terminal hydrogen on say C2, with zero charges and C2 with
> charge o
Thank you for your suggestion, but I have already tried it.
-Original Message-
From: "Pedro Alexandre de Araújo Gomes Lapido Loureiro" <[EMAIL PROTECTED]>
To: "Discussion list for GROMACS users"
Date: Mon, 5 Nov 2007 16:33:26 -0200
Subject: Re: [gmx-users] Performing simulation at air/wa
Regarding the peptide moving out of the box, it is only a visualization
artifact.
Try trjconv -pbc inbox.
2007/11/5, OZGE ENGIN <[EMAIL PROTECTED]>:
>
> Hi all,
>
> I am performing a simulation of peptide at air/water interface.
>
> The box vectors are: x,y,z where 2x=2y=z. After loading the traj
On Mon, 5 Nov 2007, David Mobley wrote:
Hi,
Everything goes fine till this point. Now, i do reverse transformations to
check for hysteresis. For vdw transformations, i get almost perfect
overlap of dG/dlambda vs lambda for forward and reverse transformations,
but for coloumb transformations, i
Hi all,
I am performing a simulation of peptide at air/water interface.
The box vectors are: x,y,z where 2x=2y=z. After loading the trajectory to the
vmd, I realized that water molecules moved out of bulk water in the z
direction: into the vacuum. However, the peptide also moved out of the bulk
Robert,
Thank you for your help, and yes I am absolutely sure that the terminal
carbons are specified as bonded in the topology file. I have used VMD and
done calculations by hand to ensure their distance is correct. I am not
applying any pressure coupling and I have also made sure that the tube
Hi,
> Everything goes fine till this point. Now, i do reverse transformations to
> check for hysteresis. For vdw transformations, i get almost perfect
> overlap of dG/dlambda vs lambda for forward and reverse transformations,
> but for coloumb transformations, if i don't use soft-core potentials,
Try using 'tinit' instead of 't_init'
-Justin
Quoting sarbani chattopadhyay <[EMAIL PROTECTED]>:
>
> Hi,
>I used 'grompp' to get the '.tpr' file for extending my run. I had
> provided the trajectory file
> , energy file for the previous run and gave the value of the last step of the
> pre
Hi,
I used 'grompp' to get the '.tpr' file for extending my run. I had provided
the trajectory file
, energy file for the previous run and gave the value of the last step of the
previous run for
the 'init_step ' and the last time step for the ' t_init' and turned
'unconstrained start'= y
Dear all:
I have a problem when I was running mdrun on different computers. I
made a .tpr file including coordinate and velocity of each atom from a crash of
mdrun and upload it to four computers whose distribution version of linux and
gcc were as follows:
computer A: Redhat
余翔 wrote:
> Dear all:
>
> I have a problem when I was running mdrun on different computers. I
> made a .tpr file including coordinate and velocity of each atom from a crash
> of mdrun and upload it to four computers whose distribution version of linux
> and gcc were as follows:
> co
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