Dear users,
Its the continuation of the question I asked yesterday, Inorder to reduce
the memory usage during g_saltbr calculations i got the trajectory of only
protein, and tpr file without water and was able to successfully run it. But
unfortunately this again got stopped at 36ns as it had
On 7/13/12 11:50 AM, Kavyashree M wrote:
Dear users,
Its the continuation of the question I asked yesterday, Inorder to reduce
the memory usage during g_saltbr calculations i got the trajectory of only
protein, and tpr file without water and was able to successfully run it. But
unfortunately
Its 50ns 25000 frames. the xtc file is 695MB. it has 16GB RAM. So will
that be insufficient? I have previously run other analysis which used to take
huge memory, for eg. covariance analysis, in a system with much lesser memory
even though CPU usage was low the job used to finish. But in this case
On 7/13/12 12:05 PM, Kavyashree M wrote:
Its 50ns 25000 frames. the xtc file is 695MB. it has 16GB RAM. So will
that be insufficient? I have previously run other analysis which used to take
huge memory, for eg. covariance analysis, in a system with much lesser memory
even though CPU usage was
Ok... I will try other options.
Thanks
Kavya
On Fri, Jul 13, 2012 at 10:23 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 7/13/12 12:05 PM, Kavyashree M wrote:
Its 50ns 25000 frames. the xtc file is 695MB. it has 16GB RAM. So will
that be insufficient? I have previously run other analysis
Dear Gromacs users,
I was running the saltbridge calculations for a dimeric
protein simulation using g_saltbr, But its taking very
long time, almost four days still its not completed.
Could anyone has suggestion regarding this issue? I am
using the same system -
Intel(R) Core(TM) i7-2600 CPU @
On 7/12/12 4:51 AM, Kavyashree M wrote:
Dear Gromacs users,
I was running the saltbridge calculations for a dimeric
protein simulation using g_saltbr, But its taking very
long time, almost four days still its not completed.
Could anyone has suggestion regarding this issue? I am
using the same
Dear Sir,
That is true as the number of the frames increased the
memory had almost reached 95% but still it has been in
95% since long and CPU usage drops down to 1.5 -2 %
but in many cases i have seen that still it will run (off course
slowly) and finish. But this was too long. So any
On 7/12/12 6:38 AM, Kavyashree M wrote:
Dear Sir,
That is true as the number of the frames increased the
memory had almost reached 95% but still it has been in
95% since long and CPU usage drops down to 1.5 -2 %
but in many cases i have seen that still it will run (off course
slowly) and
Thanks :). will check whether it makes it faster.
On Thu, Jul 12, 2012 at 4:27 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 7/12/12 6:38 AM, Kavyashree M wrote:
Dear Sir,
That is true as the number of the frames increased the
memory had almost reached 95% but still it has been in
95%
Dear Sir,
I had a problem again during g_saltbr calculation it needs
.xtc and .tpr file, I can reduce the .xtc file to have only
protein but .tpr file will have water also in it. inorder to generate
new tpr file without water using grompp, i need topology file
without water .. so do you suggest
On 7/12/12 8:15 AM, Kavyashree M wrote:
Dear Sir,
I had a problem again during g_saltbr calculation it needs
.xtc and .tpr file, I can reduce the .xtc file to have only
protein but .tpr file will have water also in it. inorder to generate
new tpr file without water using grompp, i need
I read that. but while executing tpbconv i did
not see where i can specify that i do not want
solvent?
Thanks
Kavya
On Thu, Jul 12, 2012 at 5:47 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 7/12/12 8:15 AM, Kavyashree M wrote:
Dear Sir,
I had a problem again during g_saltbr calculation
Ok may be i need to specify an index file. I will try that.
And regarding the WARNING: this .tpx file is not fully functional.
I hope it will work fine enough to finish g_saltbr calculation?
Thanks
Kavya
On Thu, Jul 12, 2012 at 5:59 PM, Kavyashree M hmkv...@gmail.com wrote:
I read that. but
On 7/12/12 8:31 AM, Kavyashree M wrote:
Ok may be i need to specify an index file. I will try that.
And regarding the WARNING: this .tpx file is not fully functional.
I hope it will work fine enough to finish g_saltbr calculation?
In principle, you should be prompted to choose a default
Dear Sir,
Thank you It worked :). a very usefull suggestion.
But it did not promt to choose any option. I used
index file.
Thank you
Kavya
On Thu, Jul 12, 2012 at 6:02 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 7/12/12 8:31 AM, Kavyashree M wrote:
Ok may be i need to specify an index
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