 |
 |
 |
 |
 |
 |
||
 |
 |
 |
 |
 |
| 5 | 1/1 | 返回列表 |
| 查看: 1563 | 回復(fù): 7 | ||
| 當(dāng)前只顯示滿足指定條件的回帖，點(diǎn)擊這里查看本話題的所有回帖 | ||
[求助]
NAMD跨膜環(huán)肽管求助，Periodic cell has become too small for original patch grid!
|
||
|
各位前輩，小妹新手一枚，學(xué)習(xí)過(guò)程中問(wèn)題多多。。。最近遇到一個(gè)棘手的問(wèn)題，還請(qǐng)大家多多幫忙。我研究的體系是跨膜環(huán)肽納米管，由于要探索納米管在脂質(zhì)膜中的傾斜，所以在模擬的過(guò)程中對(duì)脂質(zhì)膜和環(huán)肽管沒(méi)有施加任何限制，然后進(jìn)行超長(zhǎng)時(shí)間的MD模擬。 由于計(jì)算條件限制，我是以20納秒為間隔，跑完一次再接著續(xù)跑20納秒。但是實(shí)際操作后發(fā)現(xiàn)，首次二十納秒進(jìn)行順利，在進(jìn)行續(xù)跑，也就是21到40納秒的模擬時(shí)總是出現(xiàn)錯(cuò)誤，錯(cuò)誤提示是Periodic cell has become too small for original patch grid!。 我之前對(duì)照其他帖子給的方法進(jìn)行修改，增加"margin 3",改大”langevinPistonPeriod 1000. langevinPistonDecay 500“但是最后還是不行。我在這里先貼出前二十納秒的CONF和續(xù)跑的CONF文件，希望各位前輩幫忙看看問(wèn)題出在哪里，多謝。 |
回復(fù)此樓» 猜你喜歡
303求調(diào)劑
已經(jīng)有6人回復(fù)
-
306求調(diào)劑
已經(jīng)有4人回復(fù)
-
求調(diào)劑
已經(jīng)有6人回復(fù)
-
275求調(diào)劑
已經(jīng)有5人回復(fù)
-
求調(diào)劑
已經(jīng)有7人回復(fù)
-
考研調(diào)劑
已經(jīng)有4人回復(fù)
-
285求調(diào)劑
已經(jīng)有6人回復(fù)
-
一志愿北京化工大學(xué)070300 學(xué)碩336求調(diào)劑
已經(jīng)有7人回復(fù)
-
318求調(diào)劑
已經(jīng)有6人回復(fù)
-
305分求調(diào)劑（食品工程）
已經(jīng)有5人回復(fù)
» 本主題相關(guān)商家推薦: (我也要在這里推廣)
» 本主題相關(guān)價(jià)值貼推薦，對(duì)您同樣有幫助:
- 【求助】namd 出錯(cuò)Periodic cell has become too small for original patch grid!
已經(jīng)有10人回復(fù)
木有大神看到么。。。
5樓2013-11-11 09:50:01
|
structure 8pnt_mem_water.psf coordinates eq.pdb paraTypeCharmm on parameters par_all27_prot_lipid.inp parameters par_extraterms.inp set temperature 310 temperature $temperature if {0} { set inputname eq_r binCoordinates $inputname.restrart.coor binVelocities $inputname.vel ;# remove the "temperature" entry if you use this! #extendedSystem $inputname.xsc } firsttimestep 0 if {1} { cellBasisVector1 58. 0. 0. cellBasisVector2 0. 58. 0. cellBasisVector3 0. 0. 94. cellOrigin 0. 0. 0. } wrapAll on PME yes PMEGridSizeX 64 PMEGridSizeY 64 PMEGridSizeZ 100 exclude scaled1-4 cutoff 10. switching on switchdist 8. pairlistdist 12. timestep 1. nonbondedFreq 2 fullElectFrequency 4 stepspercycle 20 langevin on langevinDamping 5 langevinTemp $temperature langevinPiston on langevinPistonTarget 1. langevinPistonPeriod 1000. langevinPistonDecay 500. langevinPistonTemp $temperature useFlexibleCell yes useConstantRatio yes if {0} { constraints on consref constr.pdb conskfile constr.pdb conskcol B constraintscaling 10.0 } binaryoutput no outputName eq_1 dcdfreq 1000 xstFreq 1000 restartname eq_r_1 restartfreq 1000 binaryrestart yes outputEnergies 1000 outputtiming 1000 if {1} { minimize 10000 reinitvels $temperature } run 10000000 |
2樓2013-11-09 16:34:50
|
接下來(lái)是續(xù)跑的CONF structure 8pnt_mem.psf coordinates eq.pdb paraTypeCharmm on parameters par_all27_prot_lipid.inp parameters par_extraterms.inp set temperature 310 if {1} { set inputname eq_r_1 binCoordinates $inputname.coor binVelocities $inputname.vel ;# remove the "temperature" entry if you use this! #extendedSystem $inputname.xsc } firsttimestep 25723000 if {0} { cellBasisVector1 58. 0. 0. cellBasisVector2 0. 58. 0. cellBasisVector3 0. 0. 94. cellOrigin 0. 0. 0. PME yes PMEGridSizeX 64 PMEGridSizeY 64 PMEGridSizeZ 100 } wrapAll on margin 5 exclude scaled1-4 cutoff 10. switching on switchdist 8. pairlistdist 12. timestep 1. nonbondedFreq 2 fullElectFrequency 4 stepspercycle 20 langevin on langevinDamping 5 langevinTemp $temperature langevinPiston on langevinPistonTarget 1. langevinPistonPeriod 1000. langevinPistonDecay 500. langevinPistonTemp $temperature useFlexibleCell yes useConstantRatio yes if {0} { constraints on consref constr.pdb conskfile constr.pdb conskcol B constraintscaling 10.0 } binaryrestart yes binaryoutput no outputName eq_1_xu dcdfreq 1000 xstFreq 1000 restartname eq_r_1_xu restartfreq 1000 outputEnergies 1000 outputtiming 1000 if {0} { minimize 2000 reinitvels $temperature } run 4307000 |
3樓2013-11-09 16:35:49
4樓2013-11-09 18:24:02
| 最具人氣熱帖推薦 [查看全部] | 作者 | 回/看 | 最后發(fā)表 | |
|---|---|---|---|---|
|
[考研] 求調(diào)劑 +5 | Zhangbod 2026-03-21 | 6/300 |
|
|---|---|---|---|---|
|
[考研] 384求調(diào)劑 +3 | 子系博 2026-03-22 | 4/200 |
|
|
|
[考研] 一志愿華中科技大學(xué)071000，求調(diào)劑 +4 | 沿岸有貝殼6 2026-03-21 | 4/200 |
|
|
|
[考研] 085600材料與化工306 +4 | z1z2z3879 2026-03-21 | 4/200 |
|
|
|
[考研] 初試 317 +7 | 半拉月丙 2026-03-20 | 7/350 |
|
|
|
[考研] 一志愿南大，0703化學(xué)，分?jǐn)?shù)336，求調(diào)劑 +3 | 收到VS 2026-03-21 | 3/150 |
|
|
|
[考研] 材料學(xué)碩333求調(diào)劑 +3 | 北道巷 2026-03-18 | 3/150 |
|
|
|
[考研] 材料工程（專）一志愿985 初試335求調(diào)劑 +3 | hiloiy 2026-03-17 | 4/200 |
|
|
|
[考研] 一志愿西南交大，求調(diào)劑 +5 | 材化逐夢(mèng)人 2026-03-18 | 5/250 |
|
|
|
[考研] 350求調(diào)劑 +5 | weudhdk 2026-03-19 | 5/250 |
|
|
|
[考研] 289求調(diào)劑 +6 | 懷瑾握瑜l 2026-03-20 | 6/300 |
|
|
|
[考研] 一志愿吉林大學(xué)材料學(xué)碩321求調(diào)劑 +11 | Ymlll 2026-03-18 | 15/750 |
|
|
|
[考研]
 320求調(diào)劑0856
+3
|
不想起名字112 2026-03-19 | 3/150 |
|
|
|
[考研] 材料與化工求調(diào)劑 +7 | 為學(xué)666 2026-03-16 | 7/350 |
|
|
|
[考研] 一志愿福大288有機(jī)化學(xué)，求調(diào)劑 +3 | 小木蟲(chóng)200408204 2026-03-18 | 3/150 |
|
|
|
[考研] 344求調(diào)劑 +6 | knight344 2026-03-16 | 7/350 |
|
|
|
[考研] 材料專碩306英一數(shù)二 +10 | z1z2z3879 2026-03-16 | 13/650 |
|
|
|
[考博] 26博士申請(qǐng) +3 | 1042136743 2026-03-17 | 3/150 |
|
|
|
[考研] 一志愿蘇州大學(xué)材料工程（085601）專碩有科研經(jīng)歷三項(xiàng)國(guó)獎(jiǎng)兩個(gè)實(shí)用型專利一項(xiàng)省級(jí)立項(xiàng) +6 | 大火山小火山 2026-03-16 | 8/400 |
|
|
|
[考研] 275求調(diào)劑 +4 | 太陽(yáng)花天天開(kāi)心 2026-03-16 | 4/200 |
|