[gmx-users] Join my network on LinkedIn

LinkedIn Yi Gao requested to add you as a connection on LinkedIn: -- Chinmay, I'd like to add you to my professional network on LinkedIn. - Yi Accept invitation from Yi Gao http://www.linkedin.com/e/-85v1n9-hcsylpal-5g

[gmx-users] parallel run problem for nwall

Dear Sir, I am using nwall to run my system. My version is Gromacs 4.0.7. Interestingly, I could parallel run my system on 1 node with 4 or 8 cpus, but when I run it on multi-node PC-cluster, it always fails and gives no message at all. I wonder if you could help me to resolve this problem?

Re: [gmx-users] parallel run problem for nwall

Gromacs is running well on multi-nodes without nwall. But with nwall, it doesn't work. Yi On Thu, Sep 9, 2010 at 9:28 PM, Mark Abraham mark.abra...@anu.edu.auwrote: - Original Message - From: Yi Gao t21...@gmail.com Date: Friday, September 10, 2010 12:23 Subject: [gmx-users

[gmx-users] x2top problem of dealing with spc216 water

Hi, I used x2top to generate spc216.top. The spc216.gro file comes from Gromacs tutor directory. I use Gromacs 4.0.5 version. The command line is x2top -f scp216.gro -o scp216.top. The error message is Can not find forcefield for atom OW-1 with 2 bonds Can not find forcefield for atom OW-4 with 2

Re: [gmx-users] x2top problem of dealing with spc216 water

ions.itp [ system ] ; Name Protein [ molecules ] ; Compound#mols SOL 216 Thanks a lot! Yi On Sat, Sep 4, 2010 at 11:21 AM, Justin A. Lemkul jalem...@vt.edu wrote: Yi Gao wrote: Hi, I used x2top to generate spc216.top. The spc216.gro file comes from Gromacs tutor directory. I

Re: [gmx-users] x2top problem of dealing with spc216 water

And I have ~1500 spc water. Do I only need to add #include spc.itp in your topology? Thanks! Yi On Sat, Sep 4, 2010 at 2:53 PM, Yi Gao t21...@gmail.com wrote: Hi, Justin, Thanks for your advice! Do I need to add this part: #ifdef POSRES_WATER ; Position restraint for each water oxygen

Re: [gmx-users] x2top problem of dealing with spc216 water

Thanks a lot! On Sat, Sep 4, 2010 at 2:57 PM, Justin A. Lemkul jalem...@vt.edu wrote: Yi Gao wrote: And I have ~1500 spc water. Do I only need to add #include spc.itp in your topology? Thanks! I will reiterate the advice in my previous message - do some tutorial material on a simple