...@xray.bmc.uu.se
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] vsites, ffamber, charge groups, N-terminus,
and crashes
Berk Hess wrote:
Hi,
I just ran pdb2gmx (4.0.5 and git master) with AMBER on a test
di-peptide.
But for me all H's in the NH3 terminus always end up in different
.
Berk
Date: Wed, 30 Sep 2009 18:14:06 +0200
From: joc...@xray.bmc.uu.se
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] vsites, ffamber, charge groups, N-terminus, and
crashes
Berk Hess wrote:
Hi,
Are you 100% sure you have no other charge groups in your system
: [gmx-users] vsites, ffamber, charge groups, N-terminus,
and crashes
Berk Hess wrote:
Hi,
Are you 100% sure you have no other charge groups in your system
that consist of only virtual sites, but at least with 2 virtual sites?
Ah, you're right. One of the CG which caused the crash
: Re: [gmx-users] vsites, ffamber, charge groups, N-terminus, and
crashes
Berk Hess wrote:
Hi,
I just ran pdb2gmx (4.0.5 and git master) with AMBER on a test di-peptide.
But for me all H's in the NH3 terminus always end up in different
charge-groups.
No matter if I use v-sites
Hi,
I have been trying to use vsites with AMBER99SB, but the simulation
frequently cashes after a few hundred ps with the suspects (lincs
warnings, 1-4 distance error). I could pinpoint the problem to erroneous
charge group assignments generated by pdb2gmx at the NH3 group at the
N-terminus.
already got such a file from Bert.
Berk
Date: Wed, 30 Sep 2009 15:35:42 +0200
From: joc...@xray.bmc.uu.se
To: gmx-users@gromacs.org
Subject: [gmx-users] vsites, ffamber, charge groups, N-terminus, and crashes
Hi,
I have been trying to use vsites with AMBER99SB, but the simulation
Hi,
One question:
Are these crashes single processor, with domain decomposition, or both?
Berk
Date: Wed, 30 Sep 2009 15:35:42 +0200
From: joc...@xray.bmc.uu.se
To: gmx-users@gromacs.org
Subject: [gmx-users] vsites, ffamber, charge groups, N-terminus, and crashes
Hi,
I have been
combinations
of vsite generation
and charge groups.
I already got such a file from Bert.
Berk
Date: Wed, 30 Sep 2009 15:35:42 +0200
From: joc...@xray.bmc.uu.se
To: gmx-users@gromacs.org
Subject: [gmx-users] vsites, ffamber, charge groups, N-terminus, and
crashes
Hi,
I have been trying to use
@gromacs.org
Subject: [gmx-users] vsites, ffamber, charge groups, N-terminus, and
crashes
Hi,
I have been trying to use vsites with AMBER99SB, but the simulation
frequently cashes after a few hundred ps with the suspects (lincs
warnings, 1-4 distance error). I could pinpoint the problem to
erroneous
] vsites, ffamber, charge groups, N-terminus,
and crashes
Hi,
I have been trying to use vsites with AMBER99SB, but the simulation
frequently cashes after a few hundred ps with the suspects (lincs
warnings, 1-4 distance error). I could pinpoint the problem to
erroneous
charge group
...@xray.bmc.uu.se
To: gmx-users@gromacs.org
Subject: [gmx-users] vsites, ffamber, charge groups, N-terminus,
and crashes
Hi,
I have been trying to use vsites with AMBER99SB, but the simulation
frequently cashes after a few hundred ps with the suspects (lincs
warnings, 1-4
+0200
From: joc...@xray.bmc.uu.se
To: gmx-users@gromacs.org
Subject: [gmx-users] vsites, ffamber, charge groups, N-terminus,
and crashes
Hi,
I have been trying to use vsites with AMBER99SB, but the simulation
frequently cashes after a few hundred ps with the suspects (lincs
with the .hdb file,
while they were present for all other NH3 groups.
Berk
Date: Wed, 30 Sep 2009 16:45:39 +0200
From: joc...@xray.bmc.uu.se
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] vsites, ffamber, charge groups, N-terminus,
and crashes
Hey Berk,
I just found that the simulation
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