Re: [gmx-users] any alternative methods?

2012-08-22 Thread Albert
On 08/22/2012 08:23 AM, Mark Abraham wrote: The authors use a 200x200 grid in their first published work with this tool. What makes you think 20 is enough? (And even if it is enough, you still haven't demonstrated another calculation showing that the APL with the embedded protein should be diff

[gmx-users] pdb file error

2012-08-22 Thread Sylwia Chmielewska
Hello, I'm new in Gromacs. I'm using gromacs 4.5.3. I need help with pdb format. I use to convert my file by PRODRG and MN.CONVERT. I'm trying to create a topology file from the pdb using the pdb2gmx. I get an error. My molecules are quaternary ammonium salts. My pdb file by MN. CONVERT: HEADER

Re: [gmx-users] pdb file error

2012-08-22 Thread Justin Lemkul
On 8/22/12 7:44 AM, Sylwia Chmielewska wrote: Hello, I'm new in Gromacs. I'm using gromacs 4.5.3. I need help with pdb format. I use to convert my file by PRODRG and MN.CONVERT. I'm trying to create a topology file from the pdb using the pdb2gmx. I get an error. My molecules are quaternary a

Re: [gmx-users] any alternative methods?

2012-08-22 Thread Justin Lemkul
On 8/22/12 3:16 AM, Albert wrote: On 08/22/2012 08:23 AM, Mark Abraham wrote: The authors use a 200x200 grid in their first published work with this tool. What makes you think 20 is enough? (And even if it is enough, you still haven't demonstrated another calculation showing that the APL with

[gmx-users] NPT Equilibration error

2012-08-22 Thread Ankita naithani
Hi, I am trying to run NPT equilibration on two separate systems both with ligands present in the structure. However, I got two different errors for both of these and these are below: Fatal error: A charge group moved too far between two domain decomposition steps. Fatal error: 8 particles comm

Re: [gmx-users] NPT Equilibration error

2012-08-22 Thread Justin Lemkul
On 8/22/12 8:26 AM, Ankita naithani wrote: Hi, I am trying to run NPT equilibration on two separate systems both with ligands present in the structure. However, I got two different errors for both of these and these are below: Fatal error: A charge group moved too far between two domain deco

Re: [gmx-users] pdb file error

2012-08-22 Thread Sylwia Chmielewska
Thank you for your prompt reply. I will take to read about force field. Could you recommend websites for field force? Or other information about force field. Best Regards Sylwia - Oryginalna wiadomość - Od: "Justin Lemkul" Do: "Discussion list for GROMACS users" Wysłane: środa, 22 sierp

Re: [gmx-users] pdb file error

2012-08-22 Thread Justin Lemkul
On 8/22/12 8:48 AM, Sylwia Chmielewska wrote: Thank you for your prompt reply. I will take to read about force field. Could you recommend websites for field force? Or other information about force field. You can find primary literature for the various force fields available in Gromacs with

Re: [gmx-users] pdb file error

2012-08-22 Thread Sylwia Chmielewska
Thanks. Sylwia - Oryginalna wiadomość - Od: "Justin Lemkul" Do: "Discussion list for GROMACS users" Wysłane: środa, 22 sierpień 2012 14:56:16 Temat: Re: [gmx-users] pdb file error On 8/22/12 8:48 AM, Sylwia Chmielewska wrote: > Thank you for your prompt reply. I will take to read abou

Re: [gmx-users] any alternative methods?

2012-08-22 Thread Albert
hello Justin: thanks for reply. I've read both the paper and manual script. As indicated from the output, I found the following line: 3684.2953.8840018217 I just wondering how could it possible fro residue 368 with a value of 3.88? For the pure lipids/water case, my apology for thi

Re: [gmx-users] any alternative methods?

2012-08-22 Thread Justin Lemkul
On 8/22/12 9:12 AM, Albert wrote: hello Justin: thanks for reply. I've read both the paper and manual script. As indicated from the output, I found the following line: 3684.2953.8840018217 I just wondering how could it possible fro residue 368 with a value of 3.88? My guess wo

Re: [gmx-users] any alternative methods?

2012-08-22 Thread Albert
hello Justin: thanks for reply. I've checked this residue, it is close to protein but I am still curious for the value with 3.88. Even we also observe something 11, 13 which are the same weired to me. here is the screen shot for this residue. https://dl.dropbox.com/u/56271062/1.jpg thanks

Re: [gmx-users] any alternative methods?

2012-08-22 Thread Justin Lemkul
On 8/22/12 9:54 AM, Albert wrote: hello Justin: thanks for reply. I've checked this residue, it is close to protein but I am still curious for the value with 3.88. Even we also observe something 11, 13 which are the same weired to me. here is the screen shot for this residue. https://dl.

Re: [gmx-users] periodicity in msd calculation

2012-08-22 Thread Bala subramanian
Hi justin, Thanks for the suggestion. I will look at the code. Meanwhile I have one doubt regarding the following option of the g_msd tool. “-trestarttime 10 Time between restarting points in trajectory (ps)” What does this -trestart indicates actually. I did a small trail run on a 100p

Re: [gmx-users] periodicity in msd calculation

2012-08-22 Thread Justin Lemkul
On 8/22/12 12:12 PM, Bala subramanian wrote: Hi justin, Thanks for the suggestion. I will look at the code. Meanwhile I have one doubt regarding the following option of the g_msd tool. “-trestarttime 10 Time between restarting points in trajectory (ps)” What does this -trestart indi

[gmx-users] Problem with Gromacs 4.6 installation

2012-08-22 Thread jesmin jahan
Dear All, I am trying to install Gromacs 4.6 with -DGMX_OPENMM=ON I am getting the following errors in make install-mdrun ../mdlib/libmd_openmm.so.6: undefined reference to `omp_get_thread_num' ../mdlib/libmd_openmm.so.6: undefined reference to `omp_get_num_threads' ../mdlib/libmd_openmm.so.6: u

Re: [gmx-users] any alternative methods?

2012-08-22 Thread Albert
On 08/22/2012 03:58 PM, Justin Lemkul wrote: On 8/22/12 9:54 AM, Albert wrote: hello Justin: thanks for reply. I've checked this residue, it is close to protein but I am still curious for the value with 3.88. Even we also observe something 11, 13 which are the same weired to me. here