To answer my own question, the MacKerell website has the correct parameter
files for GROMACS to use via pdb2gmx:
http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs , put this in the
same directory.
I'm now following instructions from various gromacs mailing list posts and
tutorials.
Dear Gromacs users
I had posted a similar question recently, but I did not get any reply so I
think I did not put it correctly.
It is regarding thermodynamic integration of mutating (not decoupling ) VDW
parameters from state A to state B. Will different state B parameters have
different values
Hi all,
I have a solvated membrane with a pore and I'm basically following Justin's
tutorial on calculating free energy for an ion. There is a total of 30
configurations of the ion relative to the membrane, 15 above membrane, 15
below. The spacing between configurations is reasonable for a single
No, you are exactly right -- it does NOT include the external field
explicitly. The external field acts as a magical force here and gmx
potential would produce a potential distribution based on the resulting
charge distribution. The external field itself, once again, however, does
not exist in
Hi,
I'd like to use pdb2gmx, mainly to add virtual sites to an existing
system, either pre-equilibrated (in CHARMM) or a new system from
CHARMM-GUI. Is pdb2gmx suitable for this? The issue Im coming across is
that, choosing the CHARMM27 forcefield, the POPC lipids have a different
naming
I am confused about which potential it actually calculates. As I
understand, the electric field (external) adds a force for each charged
particle. This ought to change the ion distribution. If I read the gmx
potential documentation right, it uses the distribution of the charges in
the box to
It does exactly what it says it does. Which part is misunderstood?
Alex
On Wed, Mar 21, 2018 at 3:51 PM, Shreyas Kaptan
wrote:
> Hi.
>
> Thanks for the reply! Maybe I misunderstood the tool documentation. So what
> does it *really* do?
>
> On Wed, Mar 21, 2018 at 8:27
Hi.
Thanks for the reply! Maybe I misunderstood the tool documentation. So what
does it *really* do?
On Wed, Mar 21, 2018 at 8:27 PM, Alex wrote:
> Also, here is a message for the authors of the documentation:
>
> *-[no]spherical*(no)
>
>Calculate spherical thingie
>
>
bin/gmx -version:
:-) GROMACS - gmx, 2018.1 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Paul Bauer Herman J.C.
Berendsen
Par BjelkmarAldert van Buuren Rudi van Drunen Anton Feenstra
Gerrit Groenhof
Hi,
Thanks - we need some more information to be able to help. What does
bin/gmx -version report?
Mark
On Wed, Mar 21, 2018, 19:28 Jo wrote:
> Hello,
>
> I have had some errors with the v2018.1 installation make check. Any
> suggestions on what I can do?
>
> 8/39 Test
Also, here is a message for the authors of the documentation:
*-[no]spherical*(no)
Calculate spherical thingie
Come on, guys. :)
Alex
On 3/21/2018 1:24 PM, Alex wrote:
Two things:
1. We cannot see your attachment, upload to a file share.
2. gmx potential does not reveal the actual
Two things:
1. We cannot see your attachment, upload to a file share.
2. gmx potential does not reveal the actual potential drop due to
external electric field itself. What it does instead is described in the
utility documentation.
Alex
On 3/21/2018 12:42 PM, Shreyas Kaptan wrote:
Dear
Dear GMX users,
I am trying to use the gmx potential tool to calculate the potential
created by applying a constant electric field in the Z-direction.
I am using the 2018 gromacs version. The electric field was applied with:
electric-field-z = 0.00625 0 0 0; 0.1 V voltage for 160
Hello,
I have had some errors with the v2018.1 installation make check. Any
suggestions on what I can do?
8/39 Test #8: FFTUnitTests .***Exception: SegFault
0.01 sec
[==] Running 14 tests from 4 test cases.
[--] Global test environment set-up.
[--]
Hi
The problem remains with v2018.1
Any suggestions of things to try next?
Cheers
Gary
Test project /prd/pkgs/gromacs/gromacs-2018/build
Start 1: TestUtilsUnitTests
1/33 Test #1: TestUtilsUnitTests ... Passed0.17 sec
Start 2: TestUtilsMpiUnitTests
2/33 Test
Hi,
Please try 2018.1 and let us know, as some issues that look like these have
been resolved.
Thanks,
Mark
>> Cheers
>> Gary
>>
>>
>>
>>
>> wrndbeberhel13 :~> nvidia-smi
>> Wed Mar 21 16:25:23 2018
>>
>> +-+
>> |
Hi,
Your CMake installation is broken. You should probably install it again,
depending how you did it last time.
Mark
On Wed, Mar 21, 2018, 16:39 ali akgün wrote:
> Hello,
>
> I got an error in gromacs-5.1.5 installiation cmake part.
>
> My error is:
>
> *** glibc
Hi,
I am wondering if anyone had any suggestions to the problem below. Once built
gromacs fails to detect the GPU. There are no complaints at the actual cmake
and make steps, and all parameters seem to point to the correct cuda-9.1
folders etc. Currently persistence is turned on, but it
Hello,
I got an error in gromacs-5.1.5 installiation cmake part.
My error is:
*** glibc detected *** cmake: free(): invalid pointer: 0x009f241d
***
How to fix this error?
Thank you.
--
Gromacs Users mailing list
* Please search the archive at
Hi GROMACS users,
The official release of GROMACS 2018.1 is available!
This release fixes several issues found since 2018, and incorporates all
the fixes found in the recent 2016.5 release. We encourage all users of the
2018 series to update to 2018.1. Please see the link to the release notes
On Mar 21, 2018, at 10:15 AM, Alex wrote:
> Date: Wed, 21 Mar 2018 09:47:06 -0400
> From: Alex
> To: gmx-us...@gromacs.org
> Subject: [gmx-users] Topolbuild
> Message-ID:
>
Hi,
And doing the reading and planning for your data collection *before*
collecting data is a really great strategy.
Mark
On Wed, Mar 21, 2018 at 8:44 AM Joe Jordan wrote:
> Without knowing anything about your system this question is difficult to
> answer. Yo should
Hi,
Please don't spam the same question. If nobody knows the answer, maybe you
should think about a different question? I read this as "the documentation
says I can do what I want, so can I do what I want?"
Mark
On Wed, Mar 21, 2018 at 3:02 PM Apramita Chand
wrote:
>
Dear GROMACS users,
I want to use the geometric mean of both sigma (sigma i sigmaj)and
epsilon(epsilon i epsilon j) as a combination rule in my simulation.
According to the combination rules in the manual, the combination 3
incorporates Vii=sigma and Wii= epsilon along with geometric mean of
Dear all,
Using topolbuild the *.gro and *.top file for a GPS molecule (C_6H_14O_5Si)
were generated. In the GPS molecule there is a --Si(OH)3 group in which the
Si and H are indeed the atoms which produce problem in the topol file.
The Si and that H are named like below in the [ atom ] section ;
Hi,
On Tue, Mar 20, 2018 at 9:03 PM Jo wrote:
> Thanks everyone for your reply.
> I see your point that it could just be some error cancellation from
> constraints and parameters.
>
> I was previously using gromacs-5.1.4, and changed to gromacs-2018, and the
> drift seems
Hi everyone,
Does Gromacs ability to simulate metal surface in presence of solvent? any
method or force-field to include quantum interactions?
thanks
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Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
*
Hello,
in newer versions of Gromacs you can generate documentation from the
comments in the code using Doxygen.
This is then build and included in a local copy of the html
documentation when running `make webpage`, or `make doxygen-all`
You can then navigate the code documentation there or at
hellow Joe JordanSo glad to receive your adcives, I have installed
gromacs5.1.1, and useing gromacs for three years , but I know little about a
newer version you can use the automatically generated function documentation as
you said , could you give more details about this. any help will be
Try posting in gmx-developers.
--
Viveca
On Wed, Mar 21, 2018 at 2:56 AM, 刘杰 wrote:
> Dear all, Iam trying to add viscidity bond code to gromacsc 4.0.7. I
> found the harmonic bond code in bondfree.c ,but i could not conform which
> source document include the velocity
Without knowing anything about your system this question is difficult to
answer. Yo should start by reading the literature on your system or related
systems and see what they do.
On Tue, Mar 20, 2018 at 8:41 PM, Dilip H N
wrote:
> Hello all,
>
> I have run a
A few suggestions:
*use a newer version of gromacs; 4.x is no longer supported with bug fixes
*use find or grep to find what you want
*if you use a newer version you can use the automatically generated
function documentation to find what you want
On Wed, Mar 21, 2018 at 2:44 AM, 刘杰
I am trying to simulate amorphous organic solid system with Parrinello-Rahman
at P=1 Bar. The maximal dt value which holds molecules together is 0.0008 and
it's increasing leads to evaporation. What may be incorrect?
Berendsen works well with dt=0.001 but it isn't recommended.
mdp options for
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