nks
>>
>> Diana Lousa
>> Instituto de Tecnologia Química e Biológica
>> Universidade Nova de Lisboa
>> Av. da República – EAN,
>> 2780-157 Oeiras
>> PORTUGAL
>>
>>
>> -- Forwarded message --
>> From: Justin A. Lemkul <
Thanks for advice. I will test it.
Qiang
ggroenh wrote:
To rule out a sampling problem you can perform the simulations with
everything else frozen or position restraints. Both backwards and
forwards, and you can do it very fast, as there is nothing to
equilibrate. If there is still a discrepa
PROTECTED] <mailto:[EMAIL PROTECTED]>>
Date: 2008/6/16
Subject: Re: [gmx-users] Re: forward and reverse free energy not
consistant (Li Qiang)
To: Discussion list for GROMACS users <mailto:gmx-users@gromacs.org>>
Which GMX version are you using? There's a known bug in version
To rule out a sampling problem you can perform the simulations with
everything else frozen or position restraints. Both backwards and
forwards, and you can do it very fast, as there is nothing to
equilibrate. If there is still a discrepancy between the two paths,
you should suspect a proble
rwarded message --
From: Justin A. Lemkul <[EMAIL PROTECTED]>
Date: 2008/6/16
Subject: Re: [gmx-users] Re: forward and reverse free energy not
consistant (Li Qiang)
To: Discussion list for GROMACS users
Which GMX version are you using? There's a known bug in version 3.3.1
that has bee
Hi,
It is 3.3.3.
are the topology right? Can anybody kindly send me a topology with
similar mutation so that I can compare?
thanks a lot.
Qiang
Justin A. Lemkul wrote:
Which GMX version are you using? There's a known bug in version 3.3.1
that has been fixed in 3.3.3.
-Justin
friendli w
Which GMX version are you using? There's a known bug in version 3.3.1
that has been fixed in 3.3.3.
-Justin
friendli wrote:
Hi,
I use thermodynamics integration. The protocol is 1000step energy
minimization, 20 ps bond-constraint MD, and then 200ps MD for
collecting dgdl.
thanks
Qiang
Hi,
I use thermodynamics integration.
The protocol is 1000step energy minimization, 20 ps bond-constraint MD,
and then 200ps MD for collecting dgdl.
thanks
Qiang
Gerrit Groenhof wrote:
Looks like hysteresis. Do you do slow growth, or discrete FEP?
Gerrit
Dear all Gmxers,
I am calcula
Looks like hysteresis. Do you do slow growth, or discrete FEP?
Gerrit
Dear all Gmxers,
I am calculating a mutation free energy from L<->A for a five AA
peptides using G96 53a6 force field.
however, my dG_for and dG_rev is quite different.
dG_for(lambda=0.00) = - 9.9 kJ/mol
dG_rev(lambda=1.
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