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

2017-08-08 Thread Mahsa E
Thank you for your help! Best regards, Mahsa On Mon, Aug 7, 2017 at 4:35 PM, Justin Lemkul wrote: > > > On 8/6/17 8:35 PM, Mahsa E wrote: > >> Hello Justin, >> >> Thank you so much for your reply! >> >> I followed what you suggested. Please correct me if I misunderstood; >> >>

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

2017-08-07 Thread Justin Lemkul
On 8/6/17 8:35 PM, Mahsa E wrote: Hello Justin, Thank you so much for your reply! I followed what you suggested. Please correct me if I misunderstood; 1- I used acpype to generate the parameters (charges, atom types, and bonded parameters) for the monomer, which create many files including

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

2017-08-06 Thread Mahsa E
Hello Justin, Thank you so much for your reply! I followed what you suggested. Please correct me if I misunderstood; 1- I used acpype to generate the parameters (charges, atom types, and bonded parameters) for the monomer, which create many files including GMX_OPLS.itp , GMX_OPLS.top and

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

2017-08-05 Thread Justin Lemkul
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

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

2017-08-05 Thread Mahsa E
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

2017-08-05 Thread Mahsa E
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