eqs 19/20 were implemented for motion.
The problem was the calculation of com of a molecule splited across
boundaries.with
calc_xcm that does not check for this.
Problem solved with suggestion of Mark.
Thanks
On Mon, Dec 14, 2009 at 8:04 AM, Omer Markovitch wrote:
> See for example eq. 19 & 2
See for example eq. 19 & 20 at JCP 129, 84505 (
http://dx.doi.org/10.1063/1.2968608). Is this what you meant?
Omer.
On Mon, Dec 14, 2009 at 06:56, Mark Abraham wrote:
> I think that the problem comes from pbc handling for molecules splited
>> across boundaries - I expect : do something before ca
D D wrote:
Hi *,
I wrote a tool to calculate properties from trajectories (parallel
4.0.5), but it seems that I miss something.
In the case of MSD, I do not get the curve that g_msd produces for mol com.
On the other hand, if I run this tool for MSD on a trajectory produced
by trjconv -pbc mol
Hi *,
I wrote a tool to calculate properties from trajectories (parallel 4.0.5),
but it seems that I miss something.
In the case of MSD, I do not get the curve that g_msd produces for mol com.
On the other hand, if I run this tool for MSD on a trajectory produced by
trjconv -pbc mol,
I get the righ
seunghwan lee wrote:
Mark,
Thanks for your comments.
Well, I am running simulations with or without neutralization to see the
effect of counter ions. The troubling simulations have messages like
DD load balancing is limited by minimum cell size in dimension Z
DD step 1878999 vol min/aver 0.
pawan raghav wrote:
Hi,
Please tell me how to install GRACE source files to execute xmgrace
command to visualize 2D graph. I am unable to installed it as read from
tutorial. please help me as I am in need.
Read the link Justin provided. Nobody here can help you if you can't
demonstrate you
pawan raghav ha scritto:
> Hi,
>
> Please tell me how to install GRACE source files to execute xmgrace command
> to visualize 2D graph. I am unable to installed it as read from tutorial.
> please help me as I am in need.
>
Contact the xmgrace mailing list.
m.
--
gmx-users mailing listgmx-u
Hi,
Please tell me how to install GRACE source files to execute xmgrace command
to visualize 2D graph. I am unable to installed it as read from tutorial.
please help me as I am in need.
--
Pawan
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-us
Justin A. Lemkul wrote:
Jessé Nóbrega wrote:
Tcoupl : V-rescale
tau_t : 0.1 0.1 0.1
tc-grps: protein SOL CL-
ref_t : 300 300 300
The most immediate concern to me (besides trying to alter the
table-extension) is here. Never couple solvent and ions separately.
Please see the followi
Jessé Nóbrega wrote:
Tcoupl : V-rescale
tau_t : 0.1 0.1 0.1
tc-grps: protein SOL CL-
ref_t : 300 300 300
The most immediate concern to me (besides trying to alter the table-extension)
is here. Never couple solvent and ions separately. Please see the following:
http://www.gromacs.org
Dear
Gromacs users;
I
have got a problem when performing molecular
dynamics calculations in double precision with Gromacs Version 4.0.7.
My system contains a protein with 482 residues, water molecules and
Cl-ions.
I
have already carried out this same calculation in single precision
with succ
Hi,
Just noted that the oxygen atom types defined in opls_179 and opls_180 have
atomic numbers typed in as 7 in ffoplsaanb.itp instead of 8 (the mass
numbers are okay 15.9994 though). Accordingly, while doing QMMM, these
oxygen atoms are being recognized as Nitrogen atoms.
Biswas.
--
Pradip K B
Mark,
Thanks for your comments.
Well, I am running simulations with or without neutralization to see the
effect of counter ions. The troubling simulations have messages like
> DD load balancing is limited by minimum cell size in dimension Z
> DD step 1878999 vol min/aver 0.840! load imb.: forc
Please choose an informative subject line pertinent to the content of your
message; messages that have simply greetings often get blocked by spam filters,
and furthermore do not often rouse the interest of someone who may be able to
help you.
pawan raghav wrote:
Which files should be downloa
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