Re: [gmx-users] Generating topology file for a long polymer chain

On 8/5/17 8:12 AM, Mahsa E wrote: Dear gmx-users, I am trying to build a polymer box from scratch and generate the required input files. So far, I did these steps: 1. built a chain of the polymer 2. run ACPYPE to generate the topology file... However, since the chain is long, it took so long

Re: [gmx-users] question about gmx do_dssp

On 8/5/17 8:12 PM, Mark Abraham wrote: Hi, I'd start by checking if that last residue is a normal one... The check_oo() function in gmx_do_dssp.cpp looks like it will not work correclty for CHARMM, because it does not identify CHARMM termini, thereby ignoring the C-terminus. It looks

Re: [gmx-users] The small organic molecule occurred deformation during simulation

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Re: [gmx-users] The small organic molecule occurred deformation during simulation

Mr Justin: I have tried to do energy minimization in this situation which only existing small molecule in water, I found the structure of organic molecule didn’t become distortions. I think the distortions of organic molecules are due to these stronger interactions between small molecules

[gmx-users] Umbrella Sampling -PME

Hello, will decouple intramuscular interactions during windows simulation impact the accuracy of the PME estimated? I am pulling large molecule Regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

Re: [gmx-users] Could not find clayff forcefield

On 8/4/17 4:57 AM, G R wrote: Dear users, I try to implement Clayff forcefield for Kaolinite. I created my force field (I'm not sure about it), but gromacs couldn't find my force field in the directory. Here is my forcefield. ffnonbonded [ atomtypes ] ; name mass chargeptype

Re: [gmx-users] Gmx hbond

On 8/4/17 11:13 AM, farial tavakoli wrote: blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } Dear gromacs user I am performing protein ligand complex (t4lysosim) and now i

Re: [gmx-users] The small organic molecule occurred deformation during simulation

On 8/4/17 4:42 AM, yujie liu wrote: Hello, users I’m a novice to study the gromacs program. Now I met some problems which the small molecule occurred deformation when energy minimization was performed. For example, the anthracene molecule became bent in the plane of C-rings, the same as

Re: [gmx-users] question about gmx do_dssp

Hi, I'd start by checking if that last residue is a normal one... Mark On Sat, Aug 5, 2017 at 2:02 PM YanhuaOuyang <15901283...@163.com> wrote: > > > Dear Mark, > >Thank you, I have figure out the problem, but to my surprise, the > output xpm file lack the information of the last residue

Re: [gmx-users] QSUB commands

Hi, This a question you should answer with the online documentation for your cluster. Mark On Sat, Aug 5, 2017 at 4:28 PM Neha Gupta wrote: > Hi gromacs users, > > I use cygwin terminal in windows 7, 64 bit computer. > > How to use qsub commands and thereby do gromacs

[gmx-users] Help with segmentation fault error

Hi, I have installed 5.1.1, and am trying to run the simulations. During the run, I am getting this error as pasted below: WARNING: Listed nonbonded interaction between particles 1 and 9 at distance 9.500 which is larger than the table limit 2.030 nm. This is likely either a 1,4 interaction, or

[gmx-users] Generating topology file for a long polymer chain

Dear gmx-users, I am trying to build a polymer box from scratch and generate the required input files. So far, I did these steps: 1. built a chain of the polymer 2. run ACPYPE to generate the topology file... However, since the chain is long, it took so long time with ACPYPE and the calculation

[gmx-users] Generating topology file for a long polymer chain

Dear gmx-users, I am trying to build a polymer box from scratch and generate the required input files. So far, I did these steps: 1. built a chain of the polymer 2. run ACPYPE to generate the topology file... However, since the chain is long, it took so long time with ACPYPE and the calculation

[gmx-users] QSUB commands

Hi gromacs users, I use cygwin terminal in windows 7, 64 bit computer. How to use qsub commands and thereby do gromacs simulations in a cluster? Can anyone tell me clearly? Thanks, Neha -- Gromacs Users mailing list * Please search the archive at