Re: [gmx-users] Converting pdb from CHARMM-GUI with pdb2gmx

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.

[gmx-users] Thermodynamic integration of VDW transformation

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

[gmx-users] gmx wham

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

Re: [gmx-users] gmx potential

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

[gmx-users] pdb2gmx with CHARMM-GUI output

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

Re: [gmx-users] gmx potential

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

Re: [gmx-users] gmx potential

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

Re: [gmx-users] gmx potential

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 > >

Re: [gmx-users] gromacs 2018.1 installation

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

Re: [gmx-users] gromacs 2018.1 installation

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

Re: [gmx-users] gmx potential

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

Re: [gmx-users] gmx potential

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

[gmx-users] gmx potential

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

[gmx-users] gromacs 2018.1 installation

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. [--]

Re: [gmx-users] 2018 installation make check errors, probably CUDA related

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

Re: [gmx-users] 2018 installation make check errors, probably CUDA related

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 >> >> +-+ >> |

Re: [gmx-users] installation error

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

Re: [gmx-users] 2018 installation make check errors, probably CUDA related

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

[gmx-users] installation error

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

[gmx-users] GROMACS 2018.1 patch release available

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

Re: [gmx-users] Topolbuild

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: >

Re: [gmx-users] Regarding time steps for calculation of Hydrogen Bond Dynamics

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

Re: [gmx-users] Doubt in specifying combination rule

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: >

[gmx-users] Doubt in specifying combination rule

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

[gmx-users] Topolbuild

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 ;

Re: [gmx-users] nve energy conservation

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

[gmx-users] metal surface

Hi everyone, Does Gromacs ability to simulate metal surface in presence of solvent? any method or force-field to include quantum interactions? thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

Re: [gmx-users] source code for velocity information

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

Re: [gmx-users] source code for velocity information

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

Re: [gmx-users] source code for velocity information

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

Re: [gmx-users] Regarding time steps for calculation of Hydrogen Bond Dynamics

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

Re: [gmx-users] source code for velocity information

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

[gmx-users] Solid state barostat

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