Re: [gmx-users] Problem in installing GROMACS 2018

[Kevin Boyd]

Hi,

Did you have a previous install of gromacs 5.1.2? If so, it’s potentially a 
case of you having two installations of gromacs, and the first one found by 
your os when you try to run gmx [command] is 5.1. 

Kevin

> On May 27, 2018, at 12:10 AM, Ali Ahmed  wrote:
> 
> Dear Soham,
> I followed website instructions. I could not find instructions by Sridhar
> Manchu for 2018 version.
> Thanks
> 
>> On Sat, May 26, 2018 at 10:54 PM, Soham Sarkar  wrote:
>> 
>> Follow installation by Sridhar Manchu
>> 
>>> On Sun, 27 May 2018, 4:23 am Ali Ahmed,  wrote:
>>> 
>>> Hello GROMACS users,
>>> 
>>> I'm trying to install GROMACS 2018 on my laptop. I followed the
>>> instructions on GROMACS website and everything looks fine.
>>> But when I check the version. it says :  :-) GROMACS - gmx, VERSION 5.1.2
>>> (-: .
>>> Please, can anyone tell me how to install 2018 version? because I need to
>>> use electric field options
>>> 
>>> Thank you
>>> Ali
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>>> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Problem in installing GROMACS 2018

[Ali Ahmed]

Dear Soham,
I followed website instructions. I could not find instructions by Sridhar
Manchu for 2018 version.
Thanks

On Sat, May 26, 2018 at 10:54 PM, Soham Sarkar  wrote:

> Follow installation by Sridhar Manchu
>
> On Sun, 27 May 2018, 4:23 am Ali Ahmed,  wrote:
>
> > Hello GROMACS users,
> >
> > I'm trying to install GROMACS 2018 on my laptop. I followed the
> > instructions on GROMACS website and everything looks fine.
> > But when I check the version. it says :  :-) GROMACS - gmx, VERSION 5.1.2
> > (-: .
> > Please, can anyone tell me how to install 2018 version? because I need to
> > use electric field options
> >
> > Thank you
> > Ali
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
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>
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Re: [gmx-users] Problem in installing GROMACS 2018

[Soham Sarkar]

Follow installation by Sridhar Manchu

On Sun, 27 May 2018, 4:23 am Ali Ahmed,  wrote:

> Hello GROMACS users,
>
> I'm trying to install GROMACS 2018 on my laptop. I followed the
> instructions on GROMACS website and everything looks fine.
> But when I check the version. it says :  :-) GROMACS - gmx, VERSION 5.1.2
> (-: .
> Please, can anyone tell me how to install 2018 version? because I need to
> use electric field options
>
> Thank you
> Ali
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Problem in installing GROMACS 2018

[Ali Ahmed]

Hello Benson,
Yes, I did.

On Sat, May 26, 2018 at 9:49 PM, Benson Muite  wrote:

>
>
> On 05/27/2018 01:53 AM, Ali Ahmed wrote:
>
>> Hello GROMACS users,
>>
>> I'm trying to install GROMACS 2018 on my laptop. I followed the
>> instructions on GROMACS website and everything looks fine.
>> But when I check the version. it says :  :-) GROMACS - gmx, VERSION 5.1.2
>> (-: .
>> Please, can anyone tell me how to install 2018 version? because I need to
>> use electric field options
>>
>> Thank you
>> Ali
>>
>>
> Did you download a release version from:
> http://manual.gromacs.org/documentation/
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>
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Re: [gmx-users] Problem in installing GROMACS 2018

[Benson Muite]

On 05/27/2018 01:53 AM, Ali Ahmed wrote:

Hello GROMACS users,

I'm trying to install GROMACS 2018 on my laptop. I followed the
instructions on GROMACS website and everything looks fine.
But when I check the version. it says :  :-) GROMACS - gmx, VERSION 5.1.2
(-: .
Please, can anyone tell me how to install 2018 version? because I need to
use electric field options

Thank you
Ali



Did you download a release version from:
http://manual.gromacs.org/documentation/
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[gmx-users] Problem in installing GROMACS 2018

[Ali Ahmed]

Hello GROMACS users,

I'm trying to install GROMACS 2018 on my laptop. I followed the
instructions on GROMACS website and everything looks fine.
But when I check the version. it says :  :-) GROMACS - gmx, VERSION 5.1.2
(-: .
Please, can anyone tell me how to install 2018 version? because I need to
use electric field options

Thank you
Ali
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[gmx-users] REMD

[Eric Smoll]

Hello Gromacs Users,

I am interested in calculating the equilibrium distribution of molecular
structures at the vacuum-liquid interface of several different low vapor
pressure liquids. All of these liquids are very viscous at or near
room-temperature and I suspect that conformational barriers may inhibit
sampling at the vacuum-liquid interface. However, in NVT MD simulations,
these liquids increase fluidity at higher temperatures (400-500K) while
maintaining a fluid state and a reasonably well-defined vacuum-liquid
interface.

Can I use NVT REMD to efficiently overcome any kinetic trapping that might
be going on and obtain a true equilibrium distribution of molecular
structures at the vacuum-liquid interface? A superficial literature search
does not yield examples of NVT REMD on a liquid interface. I am curious if
there are issues or complications with this approach. Is there a better
alternative?

the manual states that "all possible pairs are tested for exchange" in
Gibbs REMD. Looking through the mdrun help output, it seems like this
option can be selected by setting the "-nex" flag. However, the comment for
this flag suggests using N^3. Isn't something like N*(N-1)/2 more
appropriate (where N is the number of replicas).

Thanks for the guidance!

Best,
Eric
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[gmx-users] Colchicine topology

[Harutyun Sahakyan]

Hi all,



I use gromacs for MD simulations, but use charmm or amber force fields, did
someone try to generate the colchicine topology? I try to do it using
CGenFF, but get to high penalty score due to dihedrals. And which force
field is better for protein-ligand simulation (tubulin-colchicine)?



Thank you in advance,

Harut
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