Hi everyone,
As I wrote yesterday, I'm having problems running stable simulations with
vsites and constraints in all bonds in different time-steps using
gmx-4.0.2. As long as the dna strand does not cross pbc, the simulations
run fine (the longest I did was 5ns). The dna topology was generated wit
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Assumpte:
De: [EMAIL PROTECTED]
Data: Tue, Novembre 25, 2008 9:52 am
A:"Discussion list for GROMACS users"
[EMAIL PROTECTED]
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On Tue, Nov 25, 2008 at 1:40 AM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
>
>
> Suman Chakrabarty wrote:
>>
>> On Mon, Nov 24, 2008 at 11:46 PM, Justin A. Lemkul <[EMAIL PROTECTED]>
>> wrote:
Tcoupl = v-rescale
tc_grps = system
tau_t
Suman Chakrabarty wrote:
On Mon, Nov 24, 2008 at 11:46 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
Tcoupl = v-rescale
tc_grps = system
tau_t= 0.1
ref_t= 300.00
Maybe you want "Protein Non-Protein" instead of "syste
On Mon, Nov 24, 2008 at 11:46 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
>> Tcoupl = v-rescale
>> tc_grps = system
>> tau_t= 0.1
>> ref_t= 300.00
>
> Maybe you want "Protein Non-Protein" instead of "system" here? But t
Hi everyone,
I'm having problems running an md simulation (with gmx-4.0.2) using vsites
and a time step of 4fs. I did generate the tpr with pdb2gmx. The problem
seems to occur when the molecule crosses pbc, since the first sign of the
simulation not working fine after ~3ns is
"
Warning: 1-4 int
[EMAIL PROTECTED] wrote:
Hi everyone,
I'm having problems running an md simulation (with gmx-4.0.2) using vsites
and a time step of 4fs. I did generate the tpr with pdb2gmx. The problem
seems to occur when the molecule crosses pbc, since the first sign of the
simulation not working fine after
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