Original Message
Subject: solaris installation error
Date: Wed, 12 Sep 2007 20:08:47 -0300
From: André Melro <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
Hello David,
2007/9/12, David van der Spoel <[EMAIL PROTECTED]>:
maybe you should try with gcc first. the performance will b
Hello David,
> 2007/9/12, David van der Spoel <[EMAIL PROTECTED]>:
> maybe you should try with gcc first. the performance will be very
> similar because of the assembly loops.
We tried that too but dont worked. diging the erros we have this call:
"bin/bash ../../../../libtool --tag=CC --mode=lin
Hi, all:
Im using g_disre in gmx3.3.1 to calculate violations of distance
restraints in a simulation and I saw the message:
Fatal error:
tpr inconsistency. ndr = 0, label = 1
The gmxdump of tpr shows
functype[459]=DISRES, label= 1, type=1, low= 1.8007e-01, up1=
2.8000
André Melro wrote:
Hi,
I'm instaling gromacs in a Sun x86 machine with Solaris 10. Configure
seams to be ok but when compiling an error ocourrs. Could any one help
me?
maybe you should try with gcc first. the performance will be very
similar because of the assembly loops.
Thanks
the conf
Wang Qin wrote:
Hi Maik,
I really did mix up a dummy atom with a virtual site. Any difference?
Thank you very much for your help.
we changed the name from dummy to virtual site a few years back. We
didn't want to be associated with MD for dummies.
Regards,
Qin
On 9/12/07,
Hi,
I'm instaling gromacs in a Sun x86 machine with Solaris 10. Configure
seams to be ok but when compiling an error ocourrs. Could any one help
me?
Thanks
the configure and compiling output:
-bash-3.00$ ./configure
checking build system type... i386-pc-solaris2.10
checking host system type...
Hi Maik,
I really did mix up a dummy atom with a virtual site. Any difference?
Thank you very much for your help.
Regards,
Qin
On 9/12/07, Maik Goette <[EMAIL PROTECTED]> wrote:
>
> The problem actually is, that you mixed up a dummy atom with a virtual
> site, I guess.
>
> Virtual si
I got a fairly good number using fluctuations formula: cv=3.91J/K.g. I
can't seem to figure out what am I doing wrong with g_energy. If
someone could run /tutor/water/spc216 and get Cv it would be greatly
appreciated.
BTW, I do get interesting numbers for that system when I run
g_energy -nmol 216
The problem actually is, that you mixed up a dummy atom with a virtual
site, I guess.
Virtual sites are not allowed to have a mass, as the error message
claims. Also, a proper hydrogen should have a mass.
If you want a hydrogen to appear, you have to place a particle in
A-state which has no
Frankie Montenegro wrote:
Correction: the number is -706.4J/mol.K (negative) . Are you sure 6 is
correct for ndf? I am running ffgmx force field and all bonds
constrained spc water.
constrained SPC water has 6 dof (3x3 - 3 constraints).
Is the temperature constant?
Maybe you do not need the -
Correction: the number is -706.4J/mol.K (negative) . Are you sure 6 is
correct for ndf? I am running ffgmx force field and all bonds
constrained spc water.
F.
On 9/12/07, Frankie Montenegro <[EMAIL PROTECTED]> wrote:
> David,
> I didn't realize what the nmol option does, thanks for the tip. But
David,
I didn't realize what the nmol option does, thanks for the tip. But
the number went from 12.5 to 706.4 (I'm hiting my forehead on my desk
as I type this). BTW why ndf 6 and not 3? For rotation?
On 9/12/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
> Frankie Montenegro wrote:
> > OK but
Frankie Montenegro wrote:
OK but I thought your number comes from equipartition theorem, not
fluctuations. I think I remember correctly someone posting the code on
the list a while ago.
Besides, I am also running 3000 SPC waters with Nose-Hoover. After
250ps, the number is identical to the one f
OK but I thought your number comes from equipartition theorem, not
fluctuations. I think I remember correctly someone posting the code on
the list a while ago.
Besides, I am also running 3000 SPC waters with Nose-Hoover. After
250ps, the number is identical to the one from the example: 12.5
J/mol.
Frankie Montenegro wrote:
I am not sure what I'm missing here. I just ran an example from
/tutor/water and got even worse
number for specific heat, around 12.5 J/mol.K. Sure, it was with
Berendsen T-coupling, no shifted VdW, but one would still expect
better number. Anyone?
Berendsen t couplin
I am not sure what I'm missing here. I just ran an example from
/tutor/water and got even worse
number for specific heat, around 12.5 J/mol.K. Sure, it was with
Berendsen T-coupling, no shifted VdW, but one would still expect
better number. Anyone?
Thanks, Frankie
_
[EMAIL PROTECTED] wrote:
Hi all
I'm simulating a helical protein in a water box, neutralized with Na and Cl to
a 0.2M comcentration. I had to pick the smallest box I could (in editconf,
rectangular, with -d 0.1, and -princ to align the box with the helix). But in
the MD trajectory I see the pr
Hi all
I'm simulating a helical protein in a water box, neutralized with Na and Cl to
a 0.2M comcentration. I had to pick the smallest box I could (in editconf,
rectangular, with -d 0.1, and -princ to align the box with the helix). But in
the MD trajectory I see the protein coming out of the bo
On 9/11/07, Mark Abraham <[EMAIL PROTECTED]> wrote:
> Frankie Montenegro wrote:
> > Hi again guys,
> >
> > Few more questions:
> >
> > 1. I would like to calculate compressibility of the protein+water
> > system, but separating it into bulk water, hydration water and
> > protein. So I need to pick
Zhou Bo wrote:
> Hi all，
>
>When I use acc_grps (e.g.: SOL), I think I should not use com motion
> removal on that group, even the whole system. Am I right?
>
yes.
>
>
> Thanks
>
>
>
>
> _
Frankie Montenegro wrote:
On 9/11/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
Frankie Montenegro wrote:
That sounds difficult because computing volume is difficult. We should
write a better program for this, but the problem lies in definition:
where does one water molecule stop and the
Hi all，
When I use acc_grps (e.g.: SOL), I think I should not use com motion
removal on that group, even the whole system. Am I right?
Thanks
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On 9/11/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
> Frankie Montenegro wrote:
> That sounds difficult because computing volume is difficult. We should
> write a better program for this, but the problem lies in definition:
> where does one water molecule stop and the next begin?
>
> >
Tha
Frankie Montenegro wrote:
Hi again guys,
Few more questions:
1. I would like to calculate compressibility of the protein+water
system, but separating it into bulk water, hydration water and
protein. So I need to pick these and compute volumes separately. When
picking hydration water molecules,
Frankie Montenegro wrote:
Hi again guys,
Few more questions:
1. I would like to calculate compressibility of the protein+water
system, but separating it into bulk water, hydration water and
protein. So I need to pick these and compute volumes separately. When
picking hydration water molecules,
Hi again guys,
Few more questions:
1. I would like to calculate compressibility of the protein+water
system, but separating it into bulk water, hydration water and
protein. So I need to pick these and compute volumes separately. When
picking hydration water molecules, two tools are mentioned on
Rui Li wrote:
Thank you for your attention.
Please keep correspondence on the list.
at the tail of pr.log, it prompts:
t = 0.052 ps: Water molecule starting at atom 35570 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous
and current coordinat
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