Hello,
I am trying to run a GROMACS simulation with few amino acids covalently bound
to Palmitoyl-linoleylphosphatidylcholine molecules., by using GROMOS ff. I
found the lipid structure and parameters on Tieleman`s website, but I don`t
know how to get the parameters for covalently bound molecu
Yes the error message indicates about the line which is in the very end ( 6 7
2 gb_27). I can see which atoms they are, 6 and 7, but I don`t know how to
solve it??? My part of top file is below, with the line it is complaining about
in bold. Thank you very much.
Include forcefield parameters
-users] free energy calculations for reference state for
constant pH MD simulations...
On 1/30/14, 2:27 PM, Ozbil, Mehmet wrote:
> For Dummy atom, I tried to write DUM for atom type and give 0 charge but it
> could not recognize the atom type. Then I just wrote the atom type with 0
> c
Lemkul
Sent: Thursday, January 30, 2014 1:43 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] free energy calculations for reference state for
constant pH MD simulations...
On 1/30/14, 1:39 PM, Ozbil, Mehmet wrote:
> By the Way, My top file looks like:
>
>
> [
proton. Only H becomes a dummy atom,
> but the C and both O atoms of the resulting COO- group will be different
> depending on protonation state. See GLU/GLUH in aminoacids.rtp.
>
> -Justin
>
>
>
>> On Thu, Jan 30, 2014 at 8:55 PM, Ozbil, Mehmet
>> wrote:
>>
&
ylate moiety
> are affected by the removal of the proton. Only H becomes a dummy atom,
> but the C and both O atoms of the resulting COO- group will be different
> depending on protonation state. See GLU/GLUH in aminoacids.rtp.
>
> -Justin
>
>
>
>> On Thu, Jan 30, 2014
f the resulting COO- group will be different depending on
protonation state. See GLU/GLUH in aminoacids.rtp.
-Justin
>
> On Thu, Jan 30, 2014 at 8:55 PM, Ozbil, Mehmet wrote:
>
>> I see Bipin,
>>
>> Thanks. One quick question though, am I going to change the charges to
1.008
You have to set the charges zero in the B state (if you want to consider
the change in electrostatic term only during deprotonation) or else change
it to DUM atom (if you want to change both the vdw and electrostatics terms
during deprotonation).
On Wed, Jan 29, 2014 at 8:15 PM, Ozbil, Mehmet
tant pH MD simulations...
See the section "5.7.4 Topologies for free energy calculations" in Gromacs
4.6.5 manual.
On Tue, Jan 28, 2014 at 3:09 AM, Ozbil, Mehmet wrote:
> Hello,
>
> I am trying to run constant pH MD with GROMACS, and started with the TI
> free energy calcula
Hello,
I am trying to run constant pH MD with GROMACS, and started with the TI free
energy calculations. I am following Justin Lemkul`s free energy calculation
tutorial, and assuming that the free energy calculations will be similar to
calculate the protonation energy of titratable amino acids
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