[gmx-users] Re: Steered Molecular Dynamics (SMD) in Gromcas-4.0.5(toby10222224 at sina.com)

Sat Jan 23 04:21:06 CET 2010

Hi Carsten:
Thank you for your answers. I don't know whether I am right to reply to gmx-users at gromacs.org. If I am wrong, please tell me.
As in my last letter, I said I was not able to set "pull_weights1" correctly. I have red the mannual, but I don't understand what it tells. I'll do with your recommendation, setting one pull group which contains 700 atoms and using Gromacs-4.0.7. Then how to set the "pull_weights1" ?
Best regards!
&nbsp;
&nbsp;
Hi,

you&nbsp;should&nbsp;set&nbsp;one&nbsp;pull&nbsp;group,&nbsp;not&nbsp;700.&nbsp;The&nbsp;number&nbsp;of&nbsp;atoms&nbsp;in&nbsp;your
pull&nbsp;group&nbsp;is&nbsp;700.&nbsp;Freezing&nbsp;the&nbsp;pull&nbsp;group&nbsp;in&nbsp;x&nbsp;and&nbsp;y&nbsp;direction&nbsp;probably
does&nbsp;what&nbsp;you&nbsp;want.&nbsp;Please&nbsp;also&nbsp;consider&nbsp;to&nbsp;upgrade&nbsp;to&nbsp;4.0.7,
which&nbsp;is&nbsp;the&nbsp;most&nbsp;recent&nbsp;stable&nbsp;version.

Best,
&nbsp;&nbsp;Carsten

On&nbsp;Jan&nbsp;22,&nbsp;2010,&nbsp;at&nbsp;7:41&nbsp;AM,&nbsp;toby10222224 at sina.com&nbsp;wrote:

>&nbsp;Dear&nbsp;all:
>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;I’m&nbsp;using&nbsp;Gromacs-4.0.5&nbsp;and&nbsp;I&nbsp;want&nbsp;to&nbsp;use&nbsp;the&nbsp;pull&nbsp;code&nbsp;to&nbsp;pull&nbsp;a&nbsp;slab&nbsp;of&nbsp;griphene&nbsp;to&nbsp;move&nbsp;along&nbsp;the&nbsp;Z&nbsp;direction&nbsp;in&nbsp;the&nbsp;simulation&nbsp;(Steered&nbsp;Molecular&nbsp;Dynamics-SMD).&nbsp;The&nbsp;griphene&nbsp;has&nbsp;700&nbsp;carbon&nbsp;atoms&nbsp;and&nbsp;the&nbsp;positions&nbsp;of&nbsp;the&nbsp;700&nbsp;atoms&nbsp;are&nbsp;expected&nbsp;to&nbsp;be&nbsp;immobile&nbsp;in&nbsp;the&nbsp;X&nbsp;and&nbsp;Y&nbsp;direction.
>&nbsp;The&nbsp;following&nbsp;is&nbsp;the&nbsp;PULL&nbsp;CODE&nbsp;in&nbsp;my&nbsp;mdp&nbsp;file.&nbsp;However,&nbsp;when&nbsp;I&nbsp;used&nbsp;this&nbsp;code&nbsp;for&nbsp;my&nbsp;simulation&nbsp;the&nbsp;error&nbsp;always&nbsp;came&nbsp;out&nbsp;as&nbsp;“Number&nbsp;of&nbsp;weights&nbsp;(1)&nbsp;for&nbsp;pull&nbsp;group&nbsp;1&nbsp;'sla'&nbsp;does&nbsp;not&nbsp;match&nbsp;the&nbsp;number&nbsp;of&nbsp;atoms&nbsp;(700)”.
>&nbsp;So&nbsp;here&nbsp;are&nbsp;my&nbsp;doubts&nbsp;about&nbsp;this&nbsp;simulation:
>&nbsp;1.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Can&nbsp;Gromacs-4.0.5&nbsp;do&nbsp;this&nbsp;for&nbsp;me,&nbsp;especially&nbsp;keeping&nbsp;the&nbsp;C&nbsp;atoms&nbsp;immobile&nbsp;in&nbsp;X&nbsp;and&nbsp;Y&nbsp;direction&nbsp;while&nbsp;moving&nbsp;along&nbsp;the&nbsp;Z&nbsp;direction?
>&nbsp;2.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;In&nbsp;my&nbsp;simulation,&nbsp;every&nbsp;carbon&nbsp;atom&nbsp;in&nbsp;the&nbsp;slab&nbsp;of&nbsp;griphene&nbsp;was&nbsp;defined&nbsp;as&nbsp;a&nbsp;group.&nbsp;Is&nbsp;it&nbsp;right?
>&nbsp;3.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;How&nbsp;to&nbsp;give&nbsp;the&nbsp;“pull_weights1”&nbsp;to&nbsp;avoid&nbsp;the&nbsp;above&nbsp;ERROR?
>&nbsp;Any&nbsp;suggestions&nbsp;and&nbsp;answers&nbsp;are&nbsp;welcome.&nbsp;Thank&nbsp;you&nbsp;in&nbsp;advance!
>&nbsp;&nbsp;
>&nbsp;;&nbsp;COM&nbsp;PULLING&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
>&nbsp;;&nbsp;Pull&nbsp;type:&nbsp;no,&nbsp;umbrella,&nbsp;constraint&nbsp;or&nbsp;constant_force
>&nbsp;pull&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=&nbsp;constant_force
>&nbsp;;&nbsp;Pull&nbsp;geometry:&nbsp;distance,&nbsp;direction,&nbsp;cylinder&nbsp;or&nbsp;position
>&nbsp;pull_geometry&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=&nbsp;distance
>&nbsp;;&nbsp;Select&nbsp;components&nbsp;for&nbsp;the&nbsp;pull&nbsp;vector.&nbsp;default:&nbsp;Y&nbsp;Y&nbsp;Y
>&nbsp;pull_dim&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=&nbsp;N&nbsp;N&nbsp;Y
>&nbsp;;&nbsp;Cylinder&nbsp;radius&nbsp;for&nbsp;dynamic&nbsp;reaction&nbsp;force&nbsp;groups&nbsp;(nm)
>&nbsp;pull_r1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=&nbsp;
>&nbsp;;&nbsp;Switch&nbsp;from&nbsp;r1&nbsp;to&nbsp;r0&nbsp;in&nbsp;case&nbsp;of&nbsp;dynamic&nbsp;reaction&nbsp;force
>&nbsp;pull_r0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=&nbsp;
>&nbsp;pull_constr_tol&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=&nbsp;1e-06
>&nbsp;pull_start&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=&nbsp;no
>&nbsp;pull_nstxout&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=&nbsp;10
>&nbsp;pull_nstfout&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=&nbsp;10
>&nbsp;;&nbsp;Number&nbsp;of&nbsp;pull&nbsp;groups&nbsp;
>&nbsp;pull_ngroups&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=&nbsp;700
>&nbsp;;&nbsp;Group&nbsp;name,&nbsp;weight&nbsp;(default&nbsp;all&nbsp;1),&nbsp;vector,&nbsp;init,&nbsp;rate&nbsp;(nm/ps),&nbsp;kJ/(mol*nm^2)
>&nbsp;pull_group0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=&nbsp;
>&nbsp;pull_weights0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=&nbsp;
>&nbsp;pull_pbcatom0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=&nbsp;
>&nbsp;pull_group1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=&nbsp;sla
>&nbsp;pull_weights1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=&nbsp;1
>&nbsp;pull_pbcatom1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=&nbsp;0
>&nbsp;pull_vec1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=&nbsp;0.0&nbsp;0.0&nbsp;1.0
>&nbsp;pull_init1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=&nbsp;0.0
>&nbsp;pull_rate1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=&nbsp;0
>&nbsp;pull_k1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=&nbsp;1.2e-4
>&nbsp;pull_kB1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=&nbsp;0
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